Not sure what is the problem. but if you have changed the name of the
first/last
residue as NXXX/CXXX, you may try to add these two names (NXXX and CXXX) to
aminoacids.dat file (also change the number in the first line).
Cheers,
Jianguo
________________________________
From: Kamesh Narasimhan <g0701...@nus.edu.sg>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Wednesday, 24 August 2011 15:10:13
Subject: RE: [gmx-users] error:You might need to add atom H to the hydrogen
database of residue
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
.
.
.
.
.
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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