[gmx-users] Deletion of Lipids During InflateGro?

Sanim Rahman sanimr at mail.usf.edu
Sun Jan 1 05:30:57 CET 2017

Thank you Justin,

Here are the commands I used:

*gmx_mpi genconf -f popc.gro -o popc_full.gro -nbox 2 1 1*

*perl inflategro.pl <http://inflategro.pl> popc_full.gro 4 POPC 1
popc_inflated.gro 5 area.dat*

The first command was used to extend the length of my bilayer and the
second was to inflate the structure. When I run the second command it reads
that there are 128 lipids in the structure. My popc.gro originally had 128
and after using the genconf command I doubled it to 256. I checked my
popc_full.gro file in VMD and opened the file in an open text editor to
ensure that it was 256 lipids.

I compared my popc_inflated.gro file to my popc.gro file inflated under the
same parameters. They were exactly the same. Thank you for your assistance.

Sanim Rahman

On Fri, Dec 30, 2016 at 11:55 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 12/29/16 10:32 PM, Sanim Rahman wrote:
>> Dear Gromacs Users,
>> I am working on building a lipid bilayer for my protein structure but I am
>> having difficulty using the InflateGRO script.
>> I am using a POPC bilayer and used the genconf command to extend the
>> length
>> of the bilayer so I would be able to go from having 128 to 256 lipids. The
>> POPC bilayer I have is already converged so I plan to inflate the bilayer
>> using InflateGRO, insert my protein in the center, and then converge to
>> the
>> appropriate lipid per area value with the script. My issue is that when I
>> inflate the bilayer the script reduces the bilayer back to 128 lipids.
>> I tried another approach by inflating my 128 lipid bilayer and then using
>> the genconf command to obtain 256 lipids. However, when converging my
>> bilayer, the lipids did not converge to the center of the entire system
>> but
>> the center of its own 128 lipid system, meaning that the bilayer split off
>> into two separate pieces.
>> Is there a way to have the script avoid reducing the number of lipids in
>> the system in my original method?
> Lipids will always be deleted by InflateGRO because some will overlap with
> the protein.  It won't delete 128 unless your protein really does occupy
> 50% of the membrane area.  Be sure you're using the right files as input.
> If you need further help, please copy and paste your exact sequence of
> commands so we can see what you're doing.
> -Justin
> --
> ==================================================
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================
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