Re: [AMBER] single -step transformation TI calculation

From: <>
Date: Sat, 10 Dec 2011 06:14:50 -0500 (EST)

Hi Victor

> This is my mdin_min_v0_l05 file:
> ................
> ifsc=1, crgmask='',scmask=':REF.A1',
> .................
> ifsc=1, crgmask='',scmask=':NEW.B1,B2',

yes, that is what I meant. Be careful though, now all atoms except A1, B1,
B2 need to have identical starting positions in both processes and they
must occur in the same order in the molecule.

> And if i'd like to do the 2-step as a comparison, I should try this:
> step1: (here use ref.prm for v1 and new.prm for v0)

your step two looks ok, but there need to be two separate charging steps.
Check out the table at:

for an example of this type. Only one of the runs would use softcore
potentials, the first and third are linear coupled between two different
charge states only.

> I hope I get the direction right. Correct me if I'm wrong. Thanks a lot.

The directions of each step dont matter, as long as you sum up the deltaGs
correctly. The important thing is that the sum of all steps needs to be
exactly your overall transformation, e.g. all changes in potential
function are explicitly considered.

Kind Regards,

Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Sat Dec 10 2011 - 03:30:05 PST
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