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Thanks Jianguo,
It doesn't seem to make a difference even if i use -ignh -- I still get the same error.
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Jianguo Li [ljg...@yahoo.com.sg] Sent: Wednesday, August 24, 2011 3:06 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] error:You might need to add atom H to the hydrogen database of residue you may need to use -ignh option in pdb2gmx.
Jianguo From: Kamesh Narasimhan <g0701...@nus.edu.sg> To: "gmx-users@gromacs.org" <gmx-users@gromacs.org> Sent: Wednesday, 24 August 2011 14:42:28 Subject: [gmx-users] error:You might need to add atom H to the hydrogen database of residue Hi all,
I am using Gromacs 4.0.5 with the forcefield amber03 in a red hat linux machine to simulate a protein-DNA complex. Eventhough I manually edited my pdb file to adhere to the amber nomenclature, I get the below error.
I have not been able to pinpoint where in the pdb file, ffamber03.rtp, and ffamber03.hdb the error could be -- if it's a nomenclature error. Would be great to receive some pointers on this.
pdb2gmx -f prim_amb.pdb -o prim_amb.gro -water spc -ff amber03
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WARNING: atom H is missing in residue GLY 1 in the pdb file
You might need to add atom H to the hydrogen database of residue GLY in the file ff???.hdb (see the manual) --------------------------------- Program pdb2gmx, VERSION 4.0.5 Source code file: pdb2top.C, line: 704
Fatal error: There were 1 missing atoms in molecule Protein_C, if you want to use this incomplete topology anyhow, use the option-missing. I get the error message complaining about a missing hydrogen in the first residue, no matter what that residue is --- say for instance even if I delete the first GLY residue from my pdb file.
krish
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