AMBER Archive (2002)

Subject: Re: Perturbation with sander : trouble in keeping perturbed part bonded to unperturbed (fwd)

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 26 2002 - 20:21:06 CDT

On Mon, Aug 26, 2002, amber_at_heimdal.compchem.ucsf.edu wrote:
>
>
> I am a phd student currently learning thermodynamic integration
> techniques to compute free energies. The system I chose is acetic acid
> perturbed to formic acid in a 511 water box.
>
>
> I checked the .top file created with saveamberparmpert : the perturbed
> part seems fine (normal number of perturbed atoms, bonds....) but the
> unperturbed part seems a bit odd to me : the part corresponding to the
> methyl fragment does not appear anymore.
> e.g
>
> %FLAG BONDS_WITHOUT_HYDROGEN
>
> %FORMAT(10I8)
>
> 3 6 2 3 9 3 0 3 4
>
> from unperturbed.top
>
> becomes
>
> %FLAG BONDS_WITHOUT_HYDROGEN
>
> %FORMAT(10I8)
>
> 3 6 2 3 9 3
>
>
> in perturbed.top

The bonds are split up in a perturbed.top file, into a set that doesn't change
when you perturb, and another set (later on in the file) that has the bonds
that change.

>
>
> (here, that means that CT-C bond is not taken in account anymore)

The CT- C bond is probably in the "perturbed bonds" section of the topology
file.

>
> Maybe this is the normal way the perturbed.top files are build, but it
> may be the sign that something is wrong with my frcmod file.
>
> I used the following one :
>
> acetic to formic acid
> MASS
> Z2 1.008 Z2 IS DUMMY PROTON (HYDROGEN)
> Z1 12.01 Z1 IS aliphatic carbon linked hydrogen
>
> NONB
> Z2 0.0 0.0
> Z1 0.0 0.0
>
> BOND
> Z1-Z2 331. 1.080
> Z1-C 331. 1.080

Where is the Z2-C bond set? Don't you need that to describe the perturbed
state? Or did you remove that bond? You should set it up, with a bond
length the same as the CT-C bond (at least to begin with).

Not having a Z2-C bond parameter could be related to what you are seeing,
although I would have to know more to be sure.

>
> Here is my input file in case that might give a clue :
>

Try turning off shake (ntc=ntf=1, or at most 2). If you are changing the
bond lengths in the perturbation, this could cause problems.

The above are just guesses...I'm not sure exactly what it causing your
problems. Please let us know if you still have difficulties.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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