[gmx-users] membrane-protein tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 7 15:12:28 CET 2011

mohsen ramezanpour wrote:
> Dear all
> I am doing Membrane -protein tutorial.
> Actually I did each step carefully,I could score down my lipids 26 times.
> But there were two problems:
> 1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said
> 2-I tried to do more iteration to make closer my area per lipid to 
> 71,But I get the following error:
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/grompp.c, line: 362
> Fatal error:
> number of coordinates in coordinate file (system_shrink26.gro, 12876)
>              does not match topology (topol.top, 6438)
> I checked and I found program has added some additional DPPC molecules 
> to my system!!

InflateGRO does not add lipids, it deletes them.  Whatever you've done has 
exactly doubled the system.  You've managed to concatenate coordinate files or 
otherwise manipulate it in some nonsensical way.  Without seeing the command you 
used it's impossible to say.


> Besides I get 32 A area per lipid for this step!!!
> Please let me know what is the reason.
> Thanks in advance
> Mohsen


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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