jayalakshmi sridhar wrote:
Dear Gromacs users,
I have a homology model of a protein. Te N-terminal is an ASP residue.
When I run the command
pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i posre.itp
I get the following error-
Atom HA in residue ASP 1 not found in rtp entry with 9 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.
The protein looks alright in Sybyl. How to get this working? Thanks for
the help.
G43a1 is a united-atom force field. Alpha-carbons are not explicitly
represented. So if you pass this structure to pdb2gmx, the program assumes you
have only the necessary atoms present. If you have unnecessary hydrogens, use
-ignh.
-Justin
Jaya
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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