[gmx-users] Lipid-protein tuturial by Lemkul

[Justin A. Lemkul]

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
> 
> 
>       
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 

-- 
========================================

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

========================================