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