# Pdb2gmx: Generating an ATP topology fails with gromos54a7.ff **URL:** \ **Category:** User discussions\ **Created:** [March 8, 2023, 9:43am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-generating-an-atp-topology-fails-with-gromos54a7-ff/5935 "2023-03-08T09:43:19Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![jbehn](https://avatars.discourse-cdn.com/v4/letter/j/ce7236/32.png) [@jbehn](https://gromacs.bioexcel.eu/u/jbehn)\ **Post date:** [March 8, 2023, 9:43am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-generating-an-atp-topology-fails-with-gromos54a7-ff/5935/1 "2023-03-08T09:43:19Z")
GROMACS version: 2022.3 GROMACS modification: No Hi, I want to simulate ATP using the GROMOS gromos54a7.ff forcefield that comes shipped with the GROMACS installation. First of all, I realized that the ATP defined in the gromos54a7.ff/aminoacids.rtp is the 3- charged molecule, but I want to use the 4- charged one. Is there a reason that the 4- charged one is not defined and what can I do to build a topology for the 4- one? Secondly, even if I try to go for the 3- version as defined in gromos54a7.ff, pdb2gmx fails with the following error ```auto atom AH3PG is missing in residue ATP 653 in the pdb file atom AH3PG is missing in residue ATP 653 in the pdb file ------------------------------------------------------- Program: gmx pdb2gmx, version 2022.3 Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1584) Fatal error: There were 1 missing atoms in molecule Other, if you want to use this incomplete topology anyhow, use the option -missing ``` My call was: gmx pdb2gmx -f atp.gro -water spce -v So somehow the Hydrogen atom at the gamma phosphate oxygen is not generated although defined in the rtp file. Interestingly, when I use the older forcefields gromos53a5.ff or gromos53a6.ff, the topology can be generated successfully. These are my .gro files that I use as input. Note that the atom names are different between gromos 53 and gromos 54: atp.gro: I do the call ‘gmx pdb2gmx -f atp.gro -water spce -v’ and select ‘14: GROMOS96 54a7 force field’. It throws the Error I described above. ```auto Gnomes, ROck Monsters And Chili Sauce 31 653ATP C4' 1 13.945 1.888 5.103 653ATP O4' 2 14.043 1.890 5.210 653ATP C1' 3 13.989 1.831 5.327 653ATP C5 4 14.117 1.995 5.626 653ATP N7 5 14.062 2.102 5.560 653ATP C8 6 14.015 2.051 5.449 653ATP N9 7 14.035 1.917 5.437 653ATP N1 8 14.224 1.867 5.785 653ATP C2 9 14.202 1.764 5.708 653ATP N3 10 14.143 1.757 5.590 653ATP C4 11 14.102 1.879 5.555 653ATP C6 12 14.182 1.990 5.749 653ATP N6 13 14.197 2.104 5.824 653ATP C2' 14 13.838 1.845 5.314 653ATP O2' 15 13.771 1.735 5.374 653ATP C3' 16 13.815 1.844 5.166 653ATP O3' 17 13.789 1.710 5.127 653ATP C5' 18 13.937 2.026 5.037 653ATP O5' 19 13.900 2.130 5.129 653ATP PA 20 13.886 2.281 5.078 653ATP O1A 21 14.013 2.323 5.013 653ATP O2A 22 13.831 2.367 5.186 653ATP O3A 23 13.777 2.263 4.964 653ATP PB 24 13.619 2.211 4.964 653ATP O1B 25 13.613 2.060 4.988 653ATP O2B 26 13.537 2.304 5.055 653ATP O3B 27 13.580 2.240 4.805 653ATP PG 28 13.487 2.357 4.734 653ATP O1G 29 13.563 2.488 4.757 653ATP O2G 30 13.479 2.316 4.587 653ATP O3G 31 13.354 2.349 4.810 0.00000 0.00000 0.00000 ``` atp\_53.gro: I do the call ‘gmx pdb2gmx -f atp\_53.gro -water spce -v’ and select ‘13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)’ It generates the topology successfully ```auto Gnomes, ROck Monsters And Chili Sauce 31 653ATP AC4* 1 13.945 1.888 5.103 653ATP AO4* 2 14.043 1.890 5.210 653ATP AC1* 3 13.989 1.831 5.327 653ATP AC5 4 14.117 1.995 5.626 653ATP AN7 5 14.062 2.102 5.560 653ATP AC8 6 14.015 2.051 5.449 653ATP AN9 7 14.035 1.917 5.437 653ATP AN1 8 14.224 1.867 5.785 653ATP AC2 9 14.202 1.764 5.708 653ATP AN3 10 14.143 1.757 5.590 653ATP AC4 11 14.102 1.879 5.555 653ATP AC6 12 14.182 1.990 5.749 653ATP AN6 13 14.197 2.104 5.824 653ATP AC2* 14 13.838 1.845 5.314 653ATP AO2* 15 13.771 1.735 5.374 653ATP AC3* 16 13.815 1.844 5.166 653ATP AO3* 17 13.789 1.710 5.127 653ATP AC5* 18 13.937 2.026 5.037 653ATP AO5* 19 13.900 2.130 5.129 653ATP APA 20 13.886 2.281 5.078 653ATP AO1A 21 14.013 2.323 5.013 653ATP AO2A 22 13.831 2.367 5.186 653ATP AO3A 23 13.777 2.263 4.964 653ATP APB 24 13.619 2.211 4.964 653ATP AO1B 25 13.613 2.060 4.988 653ATP AO2B 26 13.537 2.304 5.055 653ATP AO3B 27 13.580 2.240 4.805 653ATP APG 28 13.487 2.357 4.734 653ATP AO1G 29 13.563 2.488 4.757 653ATP AO2G 30 13.479 2.316 4.587 653ATP AO3G 31 13.354 2.349 4.810 0.00000 0.00000 0.00000 ``` Why is pdb2gmx failing for the 54a7 forcefield? Thanks a lot for your time and consideration in advance! Best Julian ---
**Author:** ![TomPiggot](https://avatars.discourse-cdn.com/v4/letter/t/77aa72/32.png) [@TomPiggot](https://gromacs.bioexcel.eu/u/TomPiggot)\ **Post date:** [March 8, 2023, 6:28pm UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-generating-an-atp-topology-fails-with-gromos54a7-ff/5935/2 "2023-03-08T18:28:24Z")
If you don’t have the hydrogen in your structure you need to get pdb2gmx to build it by using the -missing option and having an appropriate .hdb file entry. More importantly though, is there a good reason to use this force field? There are both AMBER and CHARMM ATP parameters available with the more common protonation state available that will behave better than this old GROMOS model. Plus if you’re simulating something like a protein with the ATP this will likely be better with ones of these all-atom force field families too. Cheers Tom ---
**Author:** ![jbehn](https://avatars.discourse-cdn.com/v4/letter/j/ce7236/32.png) [@jbehn](https://gromacs.bioexcel.eu/u/jbehn)\ **Post date:** [March 10, 2023, 5:21am UTC](https://gromacs.bioexcel.eu/t/pdb2gmx-generating-an-atp-topology-fails-with-gromos54a7-ff/5935/3 "2023-03-10T05:21:48Z")
Hi Tom, thanks for your answer and pointing to the more appropriate force fields. The reason why I am interested in GROMOS is that I want to do a benchmark study comparing different force fields, and I was interested how GROMOS performs. Regarding the hydrogens: In principle, I was wondering why pdb2gmx worked without issues for 53a6 but not for 54a7. Thanks for mentioning the .hdb files, I checked them and I think I found now the root cause why the gamma phosphate hydrogen is not added: While (some) atom names are changed in the .rtp definition from 53a6 to 54a7 (eg, AH3G → AH3PG), the atom names stay the same in the .hdb files (eg, AH3G → AH3G). I am quite new to GROMACS, but I would assume that this atom name mismatch causes the AH3PG to not be generated. As only some atom names are different in the .rtp files, this would also explain why some hydrogens are added as expected but the gamma phosphate one _not_. Here the excerpts from the respective files: …/top/gromos53a6.ff/aminoacids.rtp ```auto ... [ATP] [atoms] AN9 NR -0.20000 0 AC4 C 0.20000 0 AN3 NR -0.36000 1 AC2 CR1 0.36000 1 AN1 NR -0.36000 2 AC6 C 0.36000 2 AN6 NT -0.83000 3 AH61 H 0.41500 3 AH62 H 0.41500 3 AC5 C 0.00000 4 AN7 NR -0.36000 4 AC8 CR1 0.36000 4 AC1* CH1 0.20000 5 AO4* OA -0.36000 5 AC4* CH1 0.16000 5 AC2* CH1 0.15000 6 AO2* OA -0.54800 6 AH2* H 0.39800 6 AC3* CH1 0.15000 7 AO3* OA -0.54800 7 AH3* H 0.39800 7 AC5* CH2 0.00000 8 AO5* OA -0.36000 9 APA P 0.70500 9 AO1A OM -0.63500 9 AO2A OM -0.63500 9 AO3A OA -0.36000 10 APB P 0.70500 10 AO1B OM -0.63500 10 AO2B OM -0.63500 10 AO3B OA -0.36000 11 APG P 0.63000 11 AO1G OM -0.63500 11 AO2G OM -0.63500 11 AO3G OA -0.54800 11 AH3G H 0.39800 11 ... ``` …/top/gromos54a7.ff/aminoacids.rtp: ```auto ... [ATP] [atoms] AN9 NR -0.20000 0 AC4 C 0.20000 0 AN3 NR -0.36000 1 AC2 CR1 0.36000 1 AN1 NR -0.36000 2 AC6 C 0.36000 2 AN6 NT -0.83000 3 AH61 H 0.41500 3 AH62 H 0.41500 3 AC5 C 0.00000 4 AN7 NR -0.36000 4 AC8 CR1 0.36000 4 AC1* CH1 0.20000 5 AO4* OA -0.36000 5 AC4* CH1 0.16000 5 AC2* CH1 0.15000 6 AO2* OA -0.54800 6 AH2* H 0.39800 6 AC3* CH1 0.15000 7 AO3* OA -0.54800 7 AH3* H 0.39800 7 AC5* CH2 0.00000 8 AO5* OA -0.36000 9 APA P 0.70500 9 AO1PA OM -0.63500 9 AO2PA OM -0.63500 9 AO3PA OA -0.36000 10 APB P 0.70500 10 AO1PB OM -0.63500 10 AO2PB OM -0.63500 10 AO3PB OA -0.36000 11 APG P 0.63000 11 AO1PG OM -0.63500 11 AO2PG OM -0.63500 11 AO3PG OA -0.54800 11 AH3PG H 0.39800 11 ... ``` …/top/gromos53a6.ff/aminoacids.hdb: ```auto ... ATP 4 2 3 AH6 AN6 AC6 AC5 1 2 AH2* AO2* AC2* AC3* 1 2 AH3* AO3* AC3* AC2* 1 2 AH3G AO3G APG AO2G ... ``` …/top/gromos54a7.ff/aminoacids.hdb: ```auto ... ATP 4 2 3 AH6 AN6 AC6 AC5 1 2 AH2* AO2* AC2* AC3* 1 2 AH3* AO3* AC3* AC2* 1 2 AH3G AO3G APG AO2G ... ``` And indeed, when I edit the …/top/gromos54a7.ff/aminoacids.hdb to ```auto ... ATP 4 2 3 AH6 AN6 AC6 AC5 1 2 AH2* AO2* AC2* AC3* 1 2 AH3* AO3* AC3* AC2* 1 2 AH3PG AO3PG APG AO2PG ... ``` , the topology can be generated successfully.