VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun Jan 26 2014 - 16:29:06 CST

Hi Arash,

Are there any ADE residues in the PDB you are trying to make a psf from?
Nothing in what you've posted shows any hint of ADE (a nucleic acid),
but psfgen get very grumpy if it encounters a residue it knows nothing
about, which is what I think is going on. If your pdb contains argon +
other stuff, you need to load 2 topology files into psfgen, one for the
argon, and one (or more) for the rest of the structure.

-Josh Vermaas

On 01/26/2014 03:06 PM, Arash Azari wrote:
> Hello everyone,
>
> Sorry, probably it is a silly mistake. I would like to simulate a
> system of Argon atoms (liquid and gas phases) and based on the old
> threads in mailing list, I have created the topology (2 different
> files) and parameter files as follows
>
> top1:
>
> MASS 251 AR 39.948 AR ! Argon
> DEFA FIRS NONE LAST NONE
> RESI A 0.00
> ATOM AR AR 0.00
>
> END
>
> top2:
>
>
> MASS 251 AR 39.948 AR ! ARGON
> RESI A 0.00 !Argon
> GROUP
> ATOM AR AR 0.00
>
> END
>
> and the parameter file:
> !
> !V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
> !
> !epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
> !Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
> !
> !atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
> !
> !Argon
> A 0.000000 -0.238000 1.908100 ! ALLOW PEP POL ARO
> ! NMA pure solvent, adm jr., 3/3/93
>
> END
>
> and this is part of the pdb file:
>
> ATOM 1 AR AR A 1 -17.370 -17.370 -17.370 0.00 0.00
> A
> ATOM 2 AR AR A 2 -14.475 -14.475 -17.370 0.00 0.00
> A
> ATOM 3 AR AR A 3 -17.370 -14.475 -14.475 0.00 0.00
> A
> END
>
> I have tried to create psf file by deleting the VMD's default topology
> file and loading one of the created top. files, but every time psfgen
> fails with the following error:
>
> unknown residue type ADE
> ERROR: failed on end of segment
>
> I highly appreciate your recommendation.
> Thank you,
>
>
> Best regards,
> Arash
>
> --
> Arash Azari