VMD-L Mailing List

From: Olya Kravchenko (ovkrav_at_gmail.com)
Date: Thu Feb 04 2016 - 21:23:13 CST

Sorry for cluttering, I've found an error. In my psfgen script I
missed a segment line. Now it looks like this:

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

This way everything works.

Olga

On Thu, Feb 4, 2016 at 9:53 PM, Olya Kravchenko <ovkrav_at_gmail.com> wrote:
> 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
>>>>>
>>>
>>>
>>