[gmx-users] Cyclohexane as a solvent
Dr. Vitaly Chaban
vvchaban at gmail.com
Thu Jul 11 21:14:11 CEST 2013
if you prepare a separate ITP for each solvent, you will save some nerves
in the long term....
Dr. Vitaly V. Chaban
On Thu, Jul 11, 2013 at 7:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 7/11/13 8:59 AM, Shima Arasteh wrote:
>> Dear all,
>> I see cyclohexane parameters in top & par CGenFF files. Would it be
>> correct if I add this molecule to the rtp file in charmm and then use it as
>> a solvent rather than for example water?
> The .rtp mechanism is generally used for building blocks of larger
> molecules, for which topologies are built with pdb2gmx. There's nothing
> wrong with building an .rtp, but it's probably about the same work as
> building an .itp, and then you have to run pdb2gmx and modify the topology
> it gives you (from .top to .itp). Save some work and just write the .itp
> file, especially since you already have all the parameters.
> Generally, how is it possible to add a new solvent to the charmm ff
> Like you would any other standalone molecule - write an .itp for it.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Associate
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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