SPC/e water model

Dear Andrew,
I went through moltemplate to create spc/e water model data file by loading
the pdb file which I had created in the VMD already. I got the data file
for spc/e water model. But here I am unable to get files related to spc/e
water box so that I can see that water box in vmd.

If you have already installed moltemplate, then all you need to do is

1) Create a file "system.lt" with these contents:

---- "system.lt" file: ----

import "spce.lt"

wat = new SPCE [260]

---- end of "system.lt" file ----

(In this example, "260" is the number of water molecules in the PDB
file you created by vmd. Change it for your PDB)

2) Then run moltemplate this way:

moltemplate.sh -pdb YOURFILE.pdb system.lt

That's all there is to it.

This works because several of the most popular force fields (like
"oplsaa.lt" and "gaff.lt") and water models ("spce.lt" and
"tip3p_2004.lt") are included in a subdirectory that moltemplate.sh
looks in whenever it can't find a file you requested. If you get the
chance, you really should take a look at the contents of the the
"spce.lt" file (in the "force_fields" subdirectory). It includes the
settings that Steve mentioned. For one thing you may need to modify
the "spce.lt" file if later you want to mix SPC/E water with molecules
that use a slightly different (but equivalent) pair_style. (For
example, the OPLSAA force field uses pair_style lj/cut/coul/long
instead of lj/charmm/coul/long, currently used by default in spce.lt.
The "force_field_OPLSAA/waterSPCE+methane/moltemplate_files/"
directory has a customized version of "spce.lt" for use with OPLSAA.)

Unfortunately, you would not even know these files exist or where to
find them if you installed moltemplate the easy way using:

pip install moltemplate

...all of the examples and documentation will be omitted or hidden
from view. I'm not sure how to handle this issue. If I start getting
a lot more questions like this, I'll remove the pip/pypi installation
option.

Cheers

Andrew

Hello Andrew,

I have generated lammps data file (system.data) for spc/e water model through moltemplate. And I can visualize that in VMD by topo command which is as follows-

in TK console > topo readlammpsdata system.data full

Now I want to add ions in that water box. For that first we need pdb and psf files for that system as inputs to autoionize.

I have created pdb and psf files in VMD by using following commands-

animate write pdb system.pdb

animate write psf system.psf

These files has been generated successfully.

But When I did autoionize to add ions. I got error that my psf file is in charmm format & it should be in x-plor format.
I tried other commands also to get x-plor format of psf such as
writepsf x-plor system.psf
writepsf X-PLOR system.psf
writepsf card name “system-xplor.psf” xplor

but nothing happened with these commands

So first my query is that NAMD and VMD generates psf file in x-plor format by default …then why my psf file is not created in x-plor format.

And secondly how can I convert psf file format from charmm to xplor.

Thanks

Regards,

Varsha