seunghwan lee wrote:
Hi
I am new to Gromacs and going through some tutorials. I am working on
lipid-protein tutorial given by Justin Lemkul and I am stuck with the
very first step. When I execute pdb2gmx to generate .top file and .pdb
without hydrogen,
pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
I got the following message:
-------------------------------------------------------
Program pdb2gmx, VERSION 4.0.4
Source code file: pgutil.c, line: 87
Fatal error:
Atom H not found in residue 17 while adding improper
-------------------------------------------------------
I made the correction to ffG53a6.rtp file as suggested by Justin, but
apparently I am still having a problem with -NH2 residue (#17). Is there
any other corrections I need to do in order to make this work?
No other correction is necessary. If you fixed the .rtp file correctly, you
should not have any problems.
-Justin
Thanks for your help!!
Seunghwan Lee
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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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