AMBER Archive (2003)

Subject: Re: Proper torsion parameters missing?

From: Miguel de Federico (miguel_at_qorws1.uab.es)
Date: Fri Jan 24 2003 - 03:27:21 CST

 I have also had this problem, and fortunately there is a quite simple way
for solving it. In the error message from leap there is also the solution.

When it says

Please add a dummy parameter of multiplicity 2
for the non-pert types to your parameter set.
 - e.g. CT-CT-CT-CA 1 0.0 0. 2.

 You can copy "CT-CT-CT-CA 1 0.0 0. 2." as a line in the
torsions field of the dummy parameter file. Leap will complain for each
dihedral parameter missing, so you have to copy each one in the in the
parameter file. (if repeated, you can remove duplicate lines). This should
work... It worked for me...

 I hope this helps,

Miguel.

> Hi Amberlist,
>
> I would like to perform a FEP with an organik molecule. I have problems
> when saving the perturbation topology and crd file.
> I have created a dummy parameter file (frcmod), with MASS, BOND, etc.
> I loaded this file in xleap (x = loadamberparams frcmod) and want to
> save my unit. But I get the following error:
> *** Proper torsion parameters missing ***
> atom names: C41-C5-C51-C1B
> atom types: CT-CT-CT-CA =pert=> CT-CT-CA-CA
> Please add a dummy parameter of multiplicity 2
> for the non-pert types to your parameter set.
> - e.g. CT-CT-CT-CA 1 0.0 0. 2.
> (This is because multiple torsional potentials may apply to a
> single torsion, and each is perturbed individually in gibbs.)
>
> This message is repeated several times.
> I added the example given by the error message to the frcmod, but
> still receive the same error message.
>
> Does anyone have an idea as to how I can solve this problem? Any help
> would be appreciated.
>
> Sincerely,
> Heike