Tom,
Now before anything else..., do you need a CB to be defined? Doesn't
one of the atom types present suffice? There's tyrosine in most force
field already, you know, and these 'CB' atoms are merely part of the
ring.
Tsjerk
On 3/15/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Tom Lenaerts wrote:
>> Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>> parameters. But for bon, you need to specify any bonded, angle, dihedral
>> interaction that CB and CR61 have in your molecule.
>
> The structure of these files is completely unclear to me. I also didn't find
any explanation of the gromacs website. Is there a online explanation of the
format and how new entries can be added?
>
> I retrieved all information on PTR from the PRODRG server. Isn't there some
way to directly copy and paste this information in the confuguration files?
>
> Below the PTR info obtained from PRODRG
it is in the manual, chapter 5.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
