Modification of structure created by Topotools using tcl script

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1

Dear Lammps Community,

I am using Topotools for creating the psf and pdb files of methane molecules as described in Tutorial - Part 2:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial—part-2

Then I am trying to use tcl script to create a spherical shape of the set of methane molecules. However I cannot process the psf and pdb files using well-known commands:
readpsf methane_N.psf
coordpdb methane_N.pdb

I have got a following error:

2

Dear Lammps Community,

I am using Topotools for creating the psf and pdb files of methane molecules
as described in Tutorial - Part 2:
https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---part-2

Then I am trying to use tcl script to create a spherical shape of the set of
methane molecules. However I cannot process the psf and pdb files using
well-known commands:
readpsf methane_N.psf
coordpdb methane_N.pdb

I have got a following error:
-----------
psfgen) reading structure from psf file methane_N.psf
psfgen) error reading atoms from psf file

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
-----------
Could you please help me to resolve this problem?

could you please explain in which way this is related to LAMMPS??

3

Dear Axel,

could you please explain in which way this is related to LAMMPS??

I am going to use the files edited by tcl script for calculations in LAMMPS.

Thank you,
Best Regards,
Evgeniya

4

Dear Axel,

could you please explain in which way this is related to LAMMPS??

I am going to use the files edited by tcl script for calculations in LAMMPS.

huh? why on earth do you need to use psfgen for it??? that doesn't
make any sense.

5

Dear Axel,

I cannot even load a single psf file created by TopoTools using VMD console:
readpsf methane_N.psf.

Files provided by NAMD tutorials can be loaded using VMD console easily. It seems there is a difference in psf files provided by NAMD and files created by TopoTools.

Best Regards,
Evgeniya

6

again, this all has *nothing* to do with LAMMPS and thus does not
belong on this mailing list.

Dear Axel,

I cannot even load a single psf file created by TopoTools using VMD console:
readpsf methane_N.psf.

readpsf is a psfgen command

Files provided by NAMD tutorials can be loaded using VMD console easily. It seems there is a difference in psf files provided by NAMD and files created by TopoTools.

this has nothing to do with topotools. please study the VMD
documentation more carefully.

the psfgen program and the psfgen plugin in VMD require .psf files in
X-PLOR format, which is why the command fails. but the command you
quote is *not* the command to load file into _VMD_. the command for
that is "mol new filename.psf" (and "mol addfile filename.pdb" to add
the .pdb file). VMD reads many variants of .psf files, but writes out
.psf files in CHARMM format (or a NAMD extension to it).

please give me a *little* bit of credit and assume that i don't put
stuff on my homepage that does not fail in such a trivial fashion. if
you still have questions about this, please post questions to the VMD
mailing list. which is the proper place for this discussion.

thanks for your understanding,
    axel.

7

Dear Axel,

I am sorry for confusing things.
Thank you very much for your detailed explanation and clarification. I will study documentation more carefully.

Thank you,
Kind Regards,
Evgeniya