[gmx-users] POPC simulation

Jim Fonseca jf163201 at ohiou.edu
Wed May 24 20:39:10 CEST 2006

I fixed this problem a while ago and it was pretty difficult to  
figure out.  I tinkered with so many things, once I got it to work I  
didn't even know what steps I took to fix it!

Here's something to try:  GROMACS doesn't like the fact popc.itp has  
a four-character residue name (since protein residues are just three  
characters).  If you look at your .gro file, you'll probably see that  
somewhere along the line, the POPC got truncated to POP.  Try  
changing all instances of 'POPC' to 'POP' in your setup--this should  
probably just be in popc.itp (lots of occurrences) and topol.top(one  
occurrence where you list the number of POP molecules.

Please let me know if that works.


On May 24, 2006, at 1:02 PM, Arindam Ganguly wrote:

> Hi Steffen,
> thanks for the reply. this is what i have done. my topol.top looks
> like this now
> #inlcude ffgmx.itp
> inlcude popc.itp.
> as per your last reply i have copied the contents of lipid.itp to
> ffgmxbon.itp and ffgmxnb.itp without removing the contents of the
> respective file. basically just appended the files with the contents
> of the lipid.itp .
> now when i run grommp -v - -f em.mdp ,
> it still says atom type "LC3" not found,.
> i can't understand why this mistake in fact taking place. popc.itp
> file the first 3 lines after [atom]
> in fact mentions LC3. so where is the mistake. plx help. thanks.
> arindam
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> 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

More information about the gromacs.org_gmx-users mailing list