Re: [AMBER] single -step transformation TI calculation

From: <>
Date: Fri, 16 Dec 2011 12:44:13 -0500 (EST)


> ifce=1, ifsc=0, crgmask='',scmask=':REF.A1',
> ifce=1, ifsc=0, crgmask='',scmask=':NEW.B1',
> or
> ifce=1, ifsc=0, crgmask='',scmask=':REF',
> ifce=1, ifsc=0, crgmask='',scmask=':NEW',

hm, I am suprised this did work at all. scmask has no effect when ifsc=0.

You are mixing two things here: You switch off the SC potential, but still
(apparently) use two different structures. The only way this could work in
my opinion is if REF and NEW have the same number, order and starting
position of atoms. Since scmask is ignored you are effectively changing
whatever differences there are in your systems all in one go. These two
ways are therefore the same calculation, run twice. Otherwise, if your
systems have different atom numbers, it would probably be bad that this
ran at all without error message...

> So it doesn't seem right to me that I'm getting the same DV/DL values when
> you are just changing atom A1 to atom B1 and when you are changing the
> whole molecule REF to molecule NEW. Also the rms values are big.

Neither is suprising, since (I think) you do the same transformation and
done without SC potentials, it may (very system-dependent!) not be too
stable. Look at the Free Energy curves to check that.

> ifce=1, ifsc=1, crgmask='',scmask=':REF.A1',
> ifce=1, ifsc=1, crgmask='',scmask=':NEW.B1',

Thats more what I would expect for a setup. Are the rms values any smaller

> The final results from the three calculations are close (delG=0.46, -1.09,
> 0.30, expt=-0.51, all in kcal/mol). So among these 3 calculations, is one

well, each of your result is within 1kcal/mol of the experiment, which is
not bad at first glance. None of the simulations are better or worse in
principle, showing that SC potentials are not always needed. The
differences may well be from sampling, longer runs may make them converge
closer to each other.

To better judge the quality of your results, it would be useful to do some
error analysis, e.g. like in Steinbrecher, Joung and Case, J Comp Chem,

Kind Regards,

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

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Received on Fri Dec 16 2011 - 10:00:03 PST
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