[gmx-users] Re: PDB and GRO files

Vitaly V. Chaban vvchaban at gmail.com
Wed Jul 22 00:08:26 CEST 2009

> Is the result of using these programs a pdb file or gro...... would you
> please explain a little bit?
> The systems that I want to simulate are fullerene and CNT. But before that
> I
> will simulate a box of water, spce. In this case is it ok to use
> spc216.pdb

> For example I checked http://www.gromacs.org/WIKI-import/PRODRG as you
> mentioned, but I can not open links on the page. All of them (check force
> field for example) can not open with like this message "Site settings could
> not be loaded"...
> Is it the page I should use to get a pdb file for my system?? I really
> appreciate if you let me know the exact web-address to use PRODRG or xLeap
> (?).
1. spc216.pdb  should contain SPC water, not SPCE.
2. You can convert your coordinates to PDB format using almost any molecular
viewer (like MOLEKEL, VMD, etc).
3. The nanotubes files (coordinates and topologies) as well as a number of
already equilibrated systems were uploaded by me to the topology section of
the old site. I guess they are still accessible. You may also want to look
for Christopher Stiles' wonderful page with many details.

Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698
!!! Looking for a postdoctoral position !!!
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