Hi,
> This error occurs typically at the middle step, when changing H to F using
soft core potential. In addition, in the amber tutorial, the minimization
You don't need a softcore potential here. Softcore potential is useful only
when you decouple or couple interactions completely. In this case, you are
simply mutating H to F. Although you can decouple H first and couple F
later, I think this two-step procedure is unnecessary.
Anyway, I guess your problem is due to the difference in SHAKE masks between
two end states. Try applying 'noshakemask' on the mutating residue.
On Fri, Aug 26, 2011 at 12:19 PM, Victor Ma <victordsmagift.gmail.com>wrote:
> hi all
>
> I'm working on the thermodynamic integration calculation. I'm trying to
> change a CH3 group to CF3 group. I initially did this directly and the
> simulation did not converge very well. So I thought changing three heavy
> atoms at the same time might be too much. I decided to do it one by one.
> First I'd like to change CH3 to CH2F. However I'm seeing errors like this:
> vlimit exceeded for step 62685; vmax = 37.6809
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2 63 67
>
> These are the distances between C and H/F in the CH2F group. I did some
> research and tried a few things, like optimizing the initial structure,
> longer minimization, slowly raising temperature,etc. So far, none of them
> worked. I'm also seeing similar problem when I'm changing phenyl to phenol
> (H to OH). So I'm wondering if this is because the relative big
> reorganization of charge distribution between the reference compound and
> new
> compound and the bond distance and angles between the C-H and C-F are too
> different.(?)
>
> This error occurs typically at the middle step, when changing H to F using
> soft core potential. In addition, in the amber tutorial, the minimization
> for this step uses SHAKE (ntf=2, ntc=2). However it never went through in
> my
> calculation. THe program complains that you can only do steepest decent and
> "softcore potentials require ntf=1 because SHAKE constraints on some bonds
> might be removed". So i'm using "ntmin=2, ntf=1,ntc=1" instead. I'm not
> sure
> if this is causing problem.
>
> Any idea? I really appreciate it. Thanks a lot.
>
>
> Victor.
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>
--
Best,
InSuk Joung
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Received on Fri Aug 26 2011 - 10:00:03 PDT
