Atomname problem while adding a residue to a forcefield

User discussions
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GROMACS version: 2018
GROMACS modification: Yes/No

Dear Gromacs community,

I am trying to add a modified Histidine residue to the AMBER14SB forcefield. I have followed the instructions in the GROMACS webpage to do so (http://www.gromacs.org/Documentation_of_outdated_versions/How-tos/Adding_a_Residue_to_a_Force_Field) and I found a problem I am struggling to understand:

I try to use pdb2gmx with the modified forcefield and it returns the following error:

Fatal error:
Atom HAA11 not found in rtp database in residue HIH, it looks a bit like HAA1
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

The problematic atom is named HAA1 and I cannot understand why pdb2gmx reads HAA11. You can see here that there is no atom HAA11 in the forcefield:

grep “HAA1” amber14sb_parmbsc1_modHIH.ff/*
amber14sb_parmbsc1_modHIH.ff/aminoacids.hdb:2 6 HAA1 CAA C2A CBA
amber14sb_parmbsc1_modHIH.ff/aminoacids.rtp: HAA1 HC 0.01500 23
amber14sb_parmbsc1_modHIH.ff/aminoacids.rtp: CAA HAA1

grep “HAA1” minsys.gro
3HIH HAA1 29 -0.575 0.306 4.823

Could you help me understand what I am doing wrong?

Thank you very much,

Salome

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This is your issue right here. You’re telling pdb2gmx to add two H atoms, with base name HAA1, to your structure. This causes pdb2gmx to create HAA11 and HAA12 to the structure, which are then not found in the .rtp entry.

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Thanks a lot, Justin.

Salome