[gmx-users] topology file for n-propanol

[Justin Lemkul]

On Wed, Nov 20, 2013 at 4:53 PM, Ehsan Sadeghi <esa38 at sfu.ca> wrote:

> Thanks Justin. Could you explain more? You meant that I don't need
> topology file for propanol? How about g_b, g_a, g_d values?
>
>
You need a topology, but what I'm saying is that it is very easy to do.
 CH3 and CH2 groups are uncharged except the CH2-O-H group, which you can
take from serine.  Look through common functional groups across molecules -
they have the same parameters.  That is the design of GROMOS and many other
force fields.  The bonded parameters can also be taken from similar groups.
 The g_* notation corresponds to the labeling defined in ffbonded.itp - b
for bonds, a for angles, d for dihedrals.  The functional groups to which
they apply are described in ffbonded.itp.

-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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