Lucio Ricardo Montero Valenzuela wrote:
Hello,
You may try to separate the sulphate from the PDB file, to run pdb2gmx without
it, ant run the PRODRG program to calculate the topology file for the sulphate
(and also its structure in gromacs format). Then you can merge your topology
and structure files for the sulphate with the respective files for the system
without sulphate. The procedure is detailed on tutorials available in the web
for gromacs 3.2 and 4.
But be aware that PRODRG charges and charge groups often require modification,
or at the very least, validation.
And use the PRODRG 2.5 (beta) server with Gromos96 - PRODRG is for ffgmx, which
is long since deprecated.
-Justin
Best regards
Lucio Montero
Mensaje citado por Jin Hee <[email protected]>:
p {margin-top:0px;margin-bottom:0px;}
Dear all,
I want to run SO3- form that is oxidation of cys in protein (SH --> SO3-).
When I used pdb2gmx, SO3-'s atom type didn't define.
Please, does anyone have experince with SO3- and can point me to reasonable
parameter.
thanks for any comment
Jin Hee
[ÇѸÞÀÏ Express]¸ÞÀϸñ·Ï°ú ¹Ì¸®º¸±â¸¦ µ¿½Ã¿¡!
Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico
----------------------------------------------------------------
Este mensaje fue enviado desde el servidor Webmail del Instituto de
Biotecnologia.
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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
