VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Feb 04 2016 - 20:53:17 CST

I still have a problem, now with generating psf file. I'd very much
appreciate your input.

I would like to create a psf file for my simulation box that consists
of 200 argon atoms. I have generated a pdb file for argon, here is a
portion of it:

ATOM 1 AR AR A 1 18.866 14.256 9.507 0.00 0.00
ATOM 2 AR AR A 2 6.942 41.521 12.453 0.00 0.00
ATOM 3 AR AR A 3 48.095 26.528 6.211 0.00 0.00
..
..(etc.)

My topology file for argon (found in the archives where similar issue
was discussed):

*>>>>>> CHARMM topology for Argon <<<<<<<<<<
27 1
MASS 1 AR 39.95 AR ! ARGON
RESI AR 0.00 !Argon
GROUP
ATOM AR AR 0.00
END

Here is what I use to create psf:

package require psfgen
topology my_topology.inp
coordpdb argon.pdb
guesscoord
writepdb new.pdb
writepsf new.psf

After I type coordpdb argon.pdb in tk console I get warnings for all
the atoms in my pdb file:

coordpdb test.pdb
psfgen) reading coordinates from pdb file test.pdb
psfgen) no segment
psfgen) Warning: failed to set coordinate for atom AR AR:1
psfgen) no segment
psfgen) Warning: failed to set coordinate for atom AR AR:2
psfgen) no segment
psfgen) Warning: failed to set coordinate for atom AR AR:3
psfgen) no segment
..
..
(etc.)

Then guesscoord gives me:

guesscoord
psfgen) Info: guessing coordinates for 0 atoms (0 non-hydrogen)

Then empty psf and pdb files are created.

The atom names in pdb file and topology file are consistent. What am I
missing? It must be something simple that I overlook.

Thank you!!

Olga

On Sat, Jan 30, 2016 at 8:28 PM, Peter Freddolino <petefred_at_umich.edu> wrote:
> (The solvate docs also have info on this: http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/
> That page has been missed in some previous threads)
>> On Jan 29, 2016, at 3:18 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>>
>> Sorry, my mistake:
>>
>> solvate -minmax {{-50 -50 -50} {50 50 50}} -o water_box
>>
>> For non-standard solvent you can use solvate too. Just type solvate and it should give you help on that. VMD mailing list should have the info you are looking for.
>>
>>
>> Maxim
>>
>>> On Jan 29, 2016, at 13:36, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>
>>> Thanks a lot!!
>>>
>>> After running this command
>>>
>>> solvate -minmax {{-50 50 -50} {50 50 50}} -o water_box
>>>
>>> I am getting the following error:
>>>
>>> Couldn't load output files. Please make sure that you have enough disk
>>> space, and that you didn't set solvent box boundaries that would
>>> produce zero placed waters.
>>>
>>> How should I address it?
>>>
>>> Also, is there a way to create a box filled with atoms/molecules other
>>> than water?
>>>
>>>
>>> On Fri, Jan 29, 2016 at 2:26 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
>>>> package require solvate
>>>> solvate -minmax {{-50 -50 -50} {50 50 50}} -o water_box
>>>>
>>>>
>>>>
>>>>> On Jan 29, 2016, at 13:17, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
>>>>>
>>>>> Hi all,
>>>>>
>>>>> I would like to create a simple rectangular simulation box filled with
>>>>> spherical particles (such as Argon atoms) for testing purposes. What
>>>>> would be the easiest way to create such system? Is it even possible
>>>>> with vmd or namd?
>>>>>
>>>>> At this point, I can only think of using a solvate plugin and creating
>>>>> a box around small protein, then deleting the protein and
>>>>> equilibrating the box without it, but this doesn't seem optimal. Is
>>>>> there another plugin/method that would be more suitable?
>>>>>
>>>>> Thanks in advance!
>>>>>
>>>>> Olga
>>>>
>>
>>
>