VMD-L Mailing List

From: Arash Azari (arash.azari_at_gmail.com)
Date: Sun Jan 26 2014 - 15:06:16 CST

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