VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Jan 27 2014 - 11:41:08 CST

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
>