jayalakshmi sridhar wrote:
Thankyou. I was able to get .gro file. How can I specify a octahedron box
for solvation. I am unable to get the syntax of the command right with -box
and -bt.
We're not going to guess what you're doing wrong. Read editconf -h and
experiment. If you need to ask here, to get useful help you at least
have to give your inputs, outputs and why you thought something was wrong!
Makr
On Fri, Sep 11, 2009 at 10:52 AM, Justin A. Lemkul <[email protected]> wrote:
jayalakshmi sridhar wrote:
Dear Gromacs users,
I have a homology model of a protein. Te N-terminal is an ASP residue.
When I run the command
pdb2gmx -f protein.pdb -o protein.gro -ff G43a1 -p protein.top -i
posre.itp
I get the following error-
Atom HA in residue ASP 1 not found in rtp entry with 9 atoms
while sorting atoms. Maybe different protonation state.
Remove this hydrogen or choose a different protonation state.
Option -ignh will ignore all hydrogens in the input.
The protein looks alright in Sybyl. How to get this working? Thanks for
the help.
G43a1 is a united-atom force field. Alpha-carbons are not explicitly
represented. So if you pass this structure to pdb2gmx, the program assumes
you have only the necessary atoms present. If you have unnecessary
hydrogens, use -ignh.
-Justin
Jaya
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.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
Ph.D. Candidate
ICTAS Doctoral Scholar
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://lists.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
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://lists.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
_______________________________________________
gmx-users mailing list [email protected]
http://lists.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
