[gmx-users] Lipid-protein tutorial by Lemkul

[seunghwan lee]

Hi Justin,

Thank you for your answer. It made me to think again and I found the 
source of the problem (silly mistake). Thanks again!

Seunghwan Lee


--- On Fri, 10/16/09, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Lipid-protein tuturial by Lemkul
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Friday, October 16, 2009, 11:45 AM
> 
> 
> 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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