VMD-L Mailing List

From: Arash Azari (arash.azari_at_gmail.com)
Date: Mon Jan 27 2014 - 15:10:16 CST

Dear Axel, Boris, and Josh,

Thank you very much indeed for your help and recommendations.
I have changed the files and it seems it is working now!
I put the files here. (by changing the epsilon and Rmin/2 accordingly)

Topology file:

*>>>>>> CHARMM topology for Argon <<<<<<<<<<
27 1

MASS 1 AR 39.948 AR ! Argon

RESI ARA 0.00 !Argon
GROUP
ATOM AR AR 0.00
PATCHING FIRST NONE LAST NONE
END

parameter file:

*>CHARMM22 All-Hydrogen Parameter File for Proteins and Lipids <<

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme
!
!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
AR 0.000000 -0.238000 1.908100 ! ALLOW PEP POL ARO
                ! NMA pure solvent, adm jr., 3/3/93

END

sample input pdb file:
ATOM 1 AR ARA 1 -17.370 -17.370 -17.370 0.00 0.00
  AR
ATOM 2 AR ARA 2 -14.475 -14.475 -17.370 0.00 0.00
  AR

Best regards,
Arash

On Mon, Jan 27, 2014 at 7:41 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Ahh... Whoops. Yeah, there are a number of problems here now that I look
> at it again. As Boris suggested, putting a resname of A will cause
> problems, as autopsf by default aliases those to ADE, which is needed so
> many crystallographic structures will generate psf files correctly. So
> you should change the name your Argon residue in the topology file from
> "A" to "AR" to distinguish it from Adenosine. Eventually you'll need to
> change the name in your parameter file too, and specify that the
> parameter is a nonbonded parameter.
>
> -Josh Vermaas
>
> On 01/27/2014 10:14 AM, Boris Steipe wrote:
> > I don't know anything about your specific file formats, but " A" is the
> PDB three-letter resName code for adenosine in ATOM and SEQRES records. I
> am guessing this is the source of your problem.
> >
> > Boris
> >
> >
> > On 2014-01-27, at 1:51 AM, Arash Azari wrote:
> >
> >> Hi Josh,
> >>
> >> Thank you for your reply.
> >> I do not have anything else in the system, only Argon atoms.
> >> Should I change all the name from AR to something different?
> >> Does the name confusion create the problem? When psfgen aliasing Ar to
> ADE.
> >> I am using VMD 1.9.1.
> >> Thank you,
> >>
> >>
> >>
> >> Best regards,
> >> Arash
> >>
> >>
> >> On Mon, Jan 27, 2014 at 12:29 AM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
> >> 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
> >>
> >>
> >>
> >> --
> >> Arash Azari
> >
>
> 

-- 
Arash Azari