Journal of Chemistry

Journal of Chemistry / 2013 / Article
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Molecular Modeling: Advancements and Applications

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Volume 2013 |Article ID 803151 | https://doi.org/10.1155/2013/803151

Diogo de Jesus Medeiros, Wilian Augusto Cortopassi, Tanos Celmar Costa França, André Silva Pimentel, "ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server", Journal of Chemistry, vol. 2013, Article ID 803151, 6 pages, 2013. https://doi.org/10.1155/2013/803151

ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server

Academic Editor: Cristiano R. W. Guimarães
Received30 Jun 2012
Accepted03 Aug 2012
Published03 Oct 2012

Abstract

The suitable computation of accurate atomic charges for the GROMACS topology *.itp files of small molecules, generated in the PRODRG server, has been a tricky task nowadays because it does not calculate atomic charges using an ab initio method. Usually additional steps of structure optimization and charges calculation, followed by a tedious manual replacement of atomic charges in the *.itp file, are needed. In order to assist this task, we report here the ITP Adjuster 1.0, a utility program developed to perform the replacement of the PRODRG charges in the *.itp files of small molecules by ab initio charges.

1. Introduction

The GROMACS package [1] is extensively used for energy minimizations (EM) and molecular dynamics (MD) simulations of biomolecules such as proteins, nucleic acids, peptides, and drugs [211]. The input topology files used by GROMACS [1] for small molecules (*.itp files) may be generated by the server PRODRG [12]. However, these files must be adjusted for MD due to the charge group concepts adopted by PRODRG [12].

The topology files preparation for performing EM and MD simulations with GROMACS [1] is very important in investigations of biological processes involving drug interactions with their molecular targets. The force fields available for biomolecules in the literature [1316] are generally based on macromolecules, such as proteins and nucleic acids, making the preparation of consistent and reliable topology files for small ordinary molecules a challenging task. The PRODRG server [12] is a reliable tool for quickly generating topologies and coordinates of ligands in protein-ligand complexes, using the empirical GROMOS96 force field [14], from a variety of different input files. This tool has been used in several studies and a wide range of knowledge areas [1725]. This server works with the concept of charge groups, which is defined as a group of bonded atoms that sums an integer total charge. Lemkul et al. [26] investigated the quality of topologies generated by the PRODRG server [12] for small molecules for the GROMOS96 43A1 force field [14] and described their functional groups. Their results show that the atomic partial charges are critically incompatible with the GROMOS force fields. Furthermore, when we use the PRODRG [12] parameters, the behavior of the system is notably different than the one observed using the GROMOS parameters. Thus, they suggest a more consistent strategy for the calculation of partial atomic charges, avoiding the deviation of behavior in the system.

Several computer programs are available for structure optimization and charge calculations using quantum chemical calculations [2729]. The Frisch et al. software [30] has been reported as the most standard for quantum chemical calculations of small molecules [3133]. Thus, the ITP adjuster 1.0 was built to make the interface of Frisch et al. [30] with the GROMACS package [1]. However, it may also be easily modified to work with different quantum chemical softwares.

There are several problems to adjust the output files of PRODRG [12] based on Frisch et al. [30] output files (*.out files): (i) the manual edition of the topology charges is an exhausting, tedious, and time-demanding assignment and, so, very susceptible to mistakes; (ii) PRODRG [12] uses a charge group concept, differently from Frisch et al. [30] and any other quantum chemical softwares; (iii) the numbering of hydrogen atoms in the *.itp files is incompatible with the output files from quantum chemical softwares; (iv) the bonds information in the Frisch et al. [30] output files may have some inconsistencies, such as hydrogen atoms bonded to two different atoms.

The ITP Adjuster 1.0 (Figure 1) performs a quick and safe edition of the *.itp files considering the charge calculations from Frisch et al. [30] using Mulliken or Chelpg (Charges from Electrostatic Potentials) charges. It handles charges of up to six decimal places. At the end of the execution, a message box will inform the total charge of the molecule in the edited *.itp file, which may be used as a guide to detect inconsistencies between the *.itp and *.out files.

2. Materials and Methods

2.1. Considerations for Using ITP Adjuster

Some requirements for using the ITP Adjuster 1.0 are important to guarantee its proper installation and use, as discussed below.

ITP Adjuster 1.0 needs the Microsoft.Net Framework 4 or later installed for running properly. The authors recommend the Frisch et al. [30] calculations and PRODRG server [12] topology generation. It is highly desirable to have a *.pdb file with numbered atom names before submitting it to the PRODRG server [12]. It guarantees the correspondence of the atom names between the *.out and the final *.itp files. ITP Adjuster 1.0 also has a functionality named “PDB Adjustment,” which verifies a *.pdb file and, if necessary, numbers the atom names.

The hydrogen charges are based on the information of bonds presented in the Frisch et al. [30] output files, which is necessary to provide an *.itp file which is compatible with the *.out file indicated. An usual mistake occurs when the PRODRG server [12] removes hydrogen atoms from oxygen and nitrogen atoms or adds hydrogen atoms that do not exist in the *.out file. In these cases, the user must use the ADDHYD, DELHYD, PATCH, or a combination of these commands in the PRODRG server [12] in order to correct these inconsistencies before using ITP Adjuster 1.0. Not performing this strategy leads to unreliable final *.itp files and meaningless total charges.

3. Results and Discussion

3.1. Validating ITP Adjuster 1.0

We validated the ITP Adjuster 1.0 with the three common molecules in biological systems: folic acid, adenosine-5′-triphosphate (ATP), and cystein. Structures of these molecules are shown in Figure 2. First we built their 3D structures in the *.pdb format using Gauss View 4.0 and Frisch et al. [30] and submitted them to energy minimization with Frisch et al. [30] using the algorithm B3LYP/3-21G with charge chelpg, in order to generate their *.out files. Besides, the *.itp files of each molecule were generated at the PRODRG server [12]. The *.out and *.itp files were then loaded into the ITP Adjuster 1.0 to change the charges of the *.itp files generated by the PRODRG server [12] by using ab initio charges of the *.out files from Frisch et al. [30]. The results are presented in Tables 1, 2, and 3. As it can be seen, the ITP Adjuster 1.0 was able to recognize the atoms in each file. It properly adjusted the charges without modifying the positions of the atoms. The ITP Adjuster 1.0 was also tested against several other small molecules (data not shown) and, without exception, it was able to adjust charges accordingly.


NrTyperesnrresidAtomcgnrChargeMassNrType resnrresidAtomcgnrChargeMass

1CR11FOLC151 0.022 12.0110 1CR11FOLC151 0.113688 12.0110
2HC1FOLH151 0.058 1.0080 2HC1FOLH151 0.091572 1.0080
3NR1FOLN31 −0.434 14.0067 3NR1FOLN31 −0.504841 14.0067
4C1FOLC161 0.335 12.0110 4C1FOLC161 0.798970 12.0110
5NR1FOLN61 −0.434 14.0067 5NR1FOLN61 −0.821446 14.0067
6C1FOLC191 0.453 12.0110 6C1FOLC191 0.946175 12.0110
7NT1FOLN72 0.082 14.0067 7NT1FOLN72 −0.931989 14.0067
8H1FOLH722 0.027 1.0080 8H1FOLH722 0.414024 1.0080
9H1FOLH712 0.027 1.0080 9H1FOLH712 0.433222 1.0080
10NR1FOLN52 0.061 14.0067 10NR1FOLN52 −0.786769 14.0067
11H1FOLH532 0.027 1.0080 11H1FOLH532 0.414871 1.0080
12C1FOLC182 0.294 12.0110 12C1FOLC182 0.698881 12.0110
13O1FOLO42 −0.676 15.9994 13O1FOLO42 −0.485705 15.9994
14C1FOLC172 0.158 12.0110 14C1FOLC172 −0.275218 12.0110
15NR1FOLN43 −0.619 14.0067 15NR1FOLN43 −0.194434 14.0067
16C1FOLC143 0.127 12.0110 16C1FOLC143 0.172175 12.0110
17CH21FOLC133 0.161 14.0270 17CH21FOLC133 0.134163 14.0270
18N1FOLN23 0.127 14.0067 18N1FOLN23 −0.476189 14.0067
19H1FOLH223 0.021 1.0080 19H1FOLH223 0.222443 1.0080
20C1FOLC33 0.127 12.0110 20C1FOLC33 0.404365 12.0110
21CR11FOLC43 0.015 12.0110 21CR11FOLC43 −0.305799 12.0110
22HC1FOLH43 0.041 1.0080 22HC1FOLH43 0.156776 1.0080
23CR11FOLC54 0.000 12.0110 23CR11FOLC54 −0.091238 12.0110
24HC1FOLH514 0.000 1.0080 24HC1FOLH514 0.118576 1.0080
25CR11FOLC24 0.000 12.0110 25CR11FOLC24 −0.334445 12.0110
26HC1FOLH214 0.000 1.0080 26HC1FOLH214 0.172869 1.0080
27CR11FOLC14 0.000 12.0110 27CR11FOLC14 −0.022017 12.0110
28HC1FOLH114 0.000 1.0080 28HC1FOLH114 0.106113 1.0080
29C1FOLC64 0.000 12.0110 29C1FOLC64 −0.147662 12.0110
30C1FOLC75 0.429 12.0110 30C1FOLC75 0.566722 12.0110
31O1FOLO15 −0.612 15.9994 31O1FOLO15 −0.487695 15.9994
32N1FOLN15 0.176 14.0067 32N1FOLN15 −0.654534 14.0067
33H1FOLH125 0.030 1.0080 33H1FOLH125 0.322800 1.0080
34CH11FOLC85 0.229 13.0190 34CH11FOLC85 0.290274 13.0190
35C1FOLC125 0.428 12.0110 35C1FOLC125 0.640657 12.0110
36O1FOLO35 −0.612 15.9994 36O1FOLO35 −0.499644 15.9994
37OA1FOLO65 −0.149 15.9994 37OA1FOLO65 −0.637158 15.9994
38H1FOLH65 0.081 1.0080 38H1FOLH65 0.456952 1.0080
39CH21FOLC96 0.198 14.0270 39CH21FOLC96 0.004713 14.0270
40CH21FOLC106 0.198 14.0270 40CH21FOLC106 −0.014129 14.0270
41C1FOLC116 0.384 12.0110 41C1FOLC116 0.703747 12.0110
42O1FOLO26 −0.685 15.9994 42O1FOLO26 −0.512801 15.9994
43OA1FOLO56 −0.167 15.9994 43OA1FOLO56 −0.633904 15.9994
44H1FOLH526 0.072 1.0080 44H1FOLH526 0.432867 1.0080


NrTyperesnrresidAtomcgnrChargeMassNrTyperesnrresidAtomcgnrChargeMass

1OA1CYSO21 −0.180 15.9994 1OA1CYSO21 −0.553855 15.9994
2H1CYSH221 0.057 1.0080 2H1CYSH221 0.366426 1.0080
3C1CYSC31 0.372 12.0110 3C1CYSC31 0.638891 12.0110
4O1CYSO11 −0.693 15.9994 4O1CYSO11 −0.478926 15.9994
5CH11CYSC21 0.175 13.0190 5CH11CYSC21 0.098300 13.0190
6NT1CYSN11 0.066 14.0067 6NT1CYSN11 −0.630975 14.0067
7H1CYSH161 0.012 1.0080 7H1CYSH161 0.282228 1.0080
8H1CYSH151 0.012 1.0080 8H1CYSH151 0.282036 1.0080
9CH21CYSC11 0.153 14.0270 9CH21CYSC11 −0.101843 14.0270
10S1CYSS11 0.077 32.0600 10S1CYSS11 0.049643 32.0600
11H1CYSH131 −0.051 1.0080 11H1CYSH131 0.048076 1.0080


NrTyperesnrresidAtomcgnrChargeMassNrTyperesnrresidAtomcgnrChargeMass

1OA1ATP0121 −0.256 15.9994 1OA1ATP0121 −0.674862 15.9994
2H1ATPH121 0.001 1.0080 2H1ATPH121 0.395648 1.0080
3P1ATPP31 1.081 30.9738 3P1ATPP31 1.542343 30.9738
4OA1ATPO131 −0.256 15.9994 4OA1ATPO131 −0.731008 15.9994
5H1ATPH131 0.001 1.0080 5H1ATPH131 0.418396 1.0080
6OM1ATPO71 −0.151 15.9994 6OM1ATPO71 −0.606703 15.9994
7OA1ATPO61 0.246 15.9994 7OA1ATPO61 −0.781970 15.9994
8P1ATPP21 1.081 30.9738 8P1ATPP21 1.666306 30.9738
9OA1ATPO111 −0.256 15.9994 9OA1ATPO111 −0.709606 15.9994
10H1ATPH111 0.001 1.0080 10H1ATPH111 0.430751 1.0080
11OM1ATPO52 0.000 15.9994 11OM1ATPO52 −0.656411 15.9994
12OA1ATPO43 −0.191 15.9994 12OA1ATPO43 −0.836197 15.9994
13P1ATPP13 1.389 30.9738 13P1ATPP13 1.661303 30.9738
14OA1ATPO103 −0.199 15.9994 14OA1ATPO103 −0.668092 15.9994
15H1ATPH933 0.001 1.0080 15H1ATPH933 0.410779 1.0080
16OM1ATPO34 −0.177 15.9994 16OM1ATPO34 −0.641581 15.9994
17OA1ATPO24 −0.289 15.9994 17OA1ATPO24 −0.604805 15.9994
18CH21ATPC104 −0.062 12.0110 18CH21ATPC104 0.301881 12.0110
19CH11ATPC94 0.093 12.0110 19CH11ATPC94 0.289979 12.0110
20OA1ATPO14 −0.289 15.9994 20OA1ATPO14 −0.515384 15.9994
21CH11ATPC84 0.024 12.0110 21CH11ATPC84 0.189925 12.0110
22OA1ATPO84 −0.301 15.9994 22OA1ATPO84 −0.558061 15.9994
23H1ATPH824 0.001 1.0080 23H1ATPH824 0.358163 1.0080
24CH11ATPC75 0.047 12.0110 24CH11ATPC75 0.186587 12.0110
25OA1ATPO95 0.261 15.9994 25OA1ATPO95 −0.541491 15.9994
26H1ATPH925 0.001 1.0080 26H1ATPH925 0.370706 1.0080
27CH11ATPC65 0.126 12.0110 27CH11ATPC65 0.578117 12.0110
28NR1ATPN35 0.169 14.0067 28NR1ATPN35 −0.804205 14.0067
29CR11ATPC55 −0.059 12.0110 29CR11ATPC55 0.257766 12.0110
30HC1ATPH515 −0.023 1.0080 30HC1ATPH515 0.276650 1.0080
31NR1ATPN46 −0.499 14.0067 31NR1ATPN46 −0.572949 14.0067
32C1ATPC36 0.096 12.0110 32C1ATPC36 0.176370 12.0110
33C1ATPC46 0.247 12.0110 33C1ATPC46 0.666733 12.0110
34NR1ATPN26 −0.512 14.0067 34NR1ATPN26 −0.611459 14.0067
35CR11ATPC16 −0.048 12.0110 35CR11ATPC16 0.210905 12.0110
36HC1ATPH16 −0.019 1.0080 36HC1ATPH16 0.220957 1.0080
37NR1ATPN16 −0.512 14.0067 37NR1ATPN16 −0.605878 14.0067
38C1ATPC26 0.247 12.0110 38C1ATPC26 0.640460 12.0110
39NT1ATPN57 0.031 14.0270 39NT1ATPN57 −0.794455 14.0270
40H1ATPH537 −0.016 1.0080 40H1ATPH537 0.327604 1.0080
41H1ATPH527 −0.015 1.0080 41H1ATPH527 0.336786 1.0080

4. Conclusion

We reported here the development of the ITP Adjuster 1.0, a utility program built to adjust ab initio charges into *.itp files generated by the PRODRG server [12]. This utility program is already in use in our laboratory and proved to be very accurate in the interface of Frisch et al. [30] and GROMACS [1], providing a friendly user interface and a quick way to generate suitable topology files to perform EM and MD calculations with the GROMACS package [1].

This utility program is available free of charge by request at lmm@puc-rio.br.

Conflict of Interests

All the authors declare that there is no conflict of interests related to the publishing of this paper on the Journal of Chemistry or any direct financial relation with the trademarks mentioned in the paper.

Acknowledgments

The authors thank the Brazilian funding agencies CNPq (Grant no. 304187/2009-7), CAPES (Grant no. 02559/09-9), and FAPERJ (Grant nos. E-26/101.452/2010 and E-26-111.532/2008) for financial support. W. A. Cortopassi also thanks CNPq, FAPERJ, the Estudar Foundation, and DMBranco for financial support and fellowship. A. S. Pimentel and T. C. C. Franca are recipients of the FAPERJ Young Scientist of Our State award.

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Copyright © 2013 Diogo de Jesus Medeiros et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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