[gmx-users] Lipid-protein tuturial by Lemkul

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 16 17:45:39 CEST 2009

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.


> 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


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