[gmx-users] MD of lipid bilayer

[Justin Lemkul]

On 10/16/13 10:32 PM, Sathya wrote:
> Dear Justin,
>
>         I am currently working on Dynamics study of DPPC lipid bilayer and
> chromium ions..
>         I want to know how to insert chromium ions into lipid bilayer. Is
> there any software for this?
>         Please suggest some idea about how to insert chromium ions into DPPC.
>

They're just ions.  Insert them with genion.  Whether or not any force field can 
adequately describe Cr is an entirely different matter...

>         When i use DPPC in pdb2gmx directly i m getting error like DPP not
> found and what should i do now?
>         Can i use directly the DPPC layer in pdb2gmx or not? ow to rectify
> this error?
>

I assume what you're seeing is 
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database.

Either you must make the force field understand what those residues are, 
e.g.http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, 
or use pre-built topologies.  There are generally .itp files available for most 
common lipids in most of the common force fields, making life vastly easier 
since the .top is very straightforward to write by hand at that point.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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