VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Jan 27 2014 - 11:05:02 CST

On Mon, Jan 27, 2014 at 1:51 AM, Arash Azari <arash.azari_at_gmail.com> 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.

why do you even bother using psfgen for a system that has no bonds?

all you'd need to do to get a valid .psf file, is to load the pdb
file, make an atom selection for all atoms, delete any residual bonds
that VMD may have guessed, set the type and other required properties
via this selection so that the psf parser in NAMD can read the psf
file (psfgen does this automatically, but VMD is more forgiving to
incomplete psf files and will only write out information that it has
available) and you are done.

axel.

> 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 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.