If atoms are missing in the sidechains of your protein, you can try a
program like scwrl3 to rebuild all or some of the sidechains. This
will give you complete sidechains in sort of reasonable positions.
Cheers
/Per
12 aug 2008 kl. 15.04 skrev vivek sharma:
Hi David,
Thanx a lot again. can you please tell me the criteria or the
standards to do such correction or can you suggest some link or
tutorial for the same?
whether swiss pdb can help in such cases?
With Thanx,
Vivek
2008/8/12 David van der Spoel <[EMAIL PROTECTED]>
vivek sharma wrote:
Hi There,
I am new to molecular dynamics and GROMACS.
While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using
the command....
pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite
hydrogen -water spce
I got the following in the last of error.....
......
......
......
.......
N-terminus: NH3+
C-terminus: COO-
WARNING: atom CE2 not found in residue 270 while adding atom
-------------------------------------------------------
Program pdb2gmx, VERSION 3.3.3
Source code file: genhydro.c, line: 304
Fatal error:
Atom CE2 not found in residue PHE270 while adding hydrogens
-------------------------------------------------------
I tried the same with different force field and water models, but
getting the same error again and again.
any suggestion will be highly appreciated.
You have an incorrect pdb file. An atom is missing. You have to fix
it yourself.
With thanx,
Vivek
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
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
