[gmx-users] .itp file of choline molecule

Justin Lemkul jalemkul at vt.edu
Mon Dec 8 20:20:06 CET 2014

On 12/8/14 9:01 AM, soumadwip ghosh wrote:
> Dear Justin,
>                  Thank you so much for your help. I saw the lipid_topper.str
> files you mentioned about. But I have some questions. Am I supposed to
> install CHARMM 36 in my source code with those tar.gz files and then modify
> the atomtypes? Currently I am using CHARMM 27 force field and I wrote the
> problem I encountered. Where do I get my choline.pdb file? I saw the
> atomtypes mentioned over there . Do you want me to change the atomtypes in
> the atomtypes.atp of my CHARMM 27 ff directory and then do pdb2gmx to
> obtain the choline.top ? As suggested by you, I understand thet there was
> some problem with my initial pdb file. Are the topology parameters listed
> in the link compatible with all the versions of CHARMM? My questions might
> sound very stupid but I dont have much experience of working with topology
> building. It will be really helpful for me to understand if you suggest me
> what is to be done step wise.

Use CHARMM36; it is much better than CHARMM27 for lipids or lipid model 
compounds.  Get the tarball from our website and use the atom types in the 
CHARMM stream file.



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


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