[gmx-users] error:You might need to add atom H to the hydrogen database of residue

[Jianguo Li]

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 <g0701207 at nus.edu.sg>
To: Discussion list for GROMACS users <gmx-users at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf 
Of Jianguo Li [ljggmx at 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 <g0701207 at nus.edu.sg>
To: "gmx-users at gromacs.org" <gmx-users at 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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