ninoo mani wrote:
Dear gmx users
I have a protein molecule with few missing residues,
a Lys with CG, CD, CE, NZ missing atoms, and
a Val with CG1, CG2 missing atoms.
I noticed that pdb2gmx reads the pdb file and places the missing atoms.
Are you sure? I'm not aware of such a feature.
First I want to know whether gromacs places only missing atoms or it
places the entire side chain?
Second, is gromacs' repaired molecule reliable for simulation or I
should do homology modelling using other softwares to repair the molecule?
Thanks,
Ninoo
------------------------------------------------------------------------
Here’s a new way to find what you're looking for - Yahoo! Answers
<http://us.rd.yahoo.com/mail/in/yanswers/*http://in.answers.yahoo.com/>
------------------------------------------------------------------------
_______________________________________________
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
--
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
