Liu Shiyong wrote:
*.gro has no chain id information.
I can not make energy group(based on chain id) from *.gro file generated
by pdb2gmx
See the mail I just sent.
3. Don't strip H, just to add them back again :)
I have the structure minimized.pdb after EM.
minimized.pdb is output from mdrun with -c option.
I tried to feed this structure into pdb2gmx.
I got an error.
Processing chain 1 'A' (5360 atoms, 535 residues)
There are 803 donors and 760 acceptors
There are 1025 hydrogen bonds
Will use HISB for residue 212
Will use HISB for residue 223
Will use HISB for residue 277
Will use HISB for residue 280
Will use HISB for residue 374
Will use HISB for residue 380
Will use HISB for residue 386
Will use HISB for residue 398
Will use HISB for residue 425
Will use HISB for residue 440
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: ../../../../src/kernel/pdb2gmx.c, line: 421
Fatal error:
Atom HD1 in residue HISB 212 not found in rtp entry with 14 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
-------------------------------------------------------
Without -ignh, pdb2gmx expects all atoms to present and appropriately named.
This is one of the more useful error messages, since it tells you exactly how to
fix the problem.
-Justin
--
========================================
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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