[gmx-users] having problem with topology file

[Neda Rafiee]

Thanks Justin!
Yaah. I found the appropriate force field in related section in ATB website with this name: gromos54a7_atb.ff.tar

And this is what I wanted!
Thanks a lot


----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Sunday, January 29, 2017 5:46:34 PM
Subject: Re: [gmx-users] having problem with topology file



On 1/28/17 12:57 PM, Neda Rafiee wrote:
> Hi. I have problem in building topology file for my system which is a pre-equilibrated membrane adopted from ATB . I have the .gro file and I need to have the topology file to do rest of my simulation. I did not find the top file in ATB website . So I am using g_x2top to do this, but I face with this error:
>
> Fatal error:
> No or incorrect atomname2type.n2t file found (looking for ./gromos45a3_lipid.ff)
>
> I am using altered Gromos45a3.ff which I added Burger lipid.itp , dppc.itp and dopc.itp parameters to it according to the tutorial for "KALP-15 in DPPC" bu Justin Lemkul.

If ATB is providing you with files for lipids, it should also give you the lipid 
parameters.  Otherwise, consult the literature for a proper topology, rather 
than trying to reinvent one with x2top.  GROMOS force fields do not have .n2t 
files built in, so you would have to build a correct one yourself, which still 
requires you to know everything about the topology.

-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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