VMD-L Mailing List

From: Boris Steipe (boris.steipe_at_utoronto.ca)
Date: Mon Jan 27 2014 - 10:14:28 CST

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