[gmx-users] Problem with adding H using amber03

[Justin A. Lemkul]

Peggy Yao wrote:
> Dear all,
> 
> I am trying to use amber03 force field. I corrected the amino acid names 
> as described on http://chemistry.csulb.edu/ffamber/.
> 
> However, when I ran pdb2gmx on a PDB file without H-atoms, I got the 
> following error:
> 
> pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb
> 
> ...
> WARNING: atom H is missing in residue THR 1 in the pdb file
>          You might need to add atom H to the hydrogen database of 
> residue THR
>          in the file ff???.hdb (see the manual)
> 

Obviously you did not follow all of the directions.  If Thr is amino acid 1 
(i.e., the N-terminus) it should be called NTHR.

-Justin

> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.2
> Source code file: pdb2top.c, line: 701
> 
> Fatal error:
> There were 1 missing atoms in molecule Protein_A, if you want to use 
> this incomplete topology anyhow, use the option -missing
> -------------------------------------------------------
> 
> I checked the ffamber03.hdb. It is in the correct directory as other 
> *.hdb files. It also contains the entry for H-atom in THR:
> 
> THR     5
> 1       1       H       N       -C      CA
> 1       5       HA      CA      N       CB      C
> 1       5       HB      CB      CA      CG2     OG1
> 3       4       HG2     CG2     CB      CA
> 1       2       HG1     OG1     CB      CA
> 
> Can anyone tell me what might be the problem? I should be able to use 
> pdb2gmx and amber03 to add all H-atoms, right?
> 
> Thanks!
> 
> Peggy
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================