You do not want to use the ffgmx forcefield. For simulating DNA and protein
i would use the amber force field. For more info on the ffamber ports see:
http://folding.stanford.edu/ffamber/
Tom
--On Wednesday, May 30, 2007 04:17:26 -0700 Alaguraj Veluchamy
<[EMAIL PROTECTED]> wrote:
Dear gmx-users,
I am trying to run a simulation of a pdb with DNA molecule.
I have give gromacs force fied and the error i found was,
There are 5 chains and 0 blocks of water and 372 residues with 3341 atoms
chain #res #atoms
1 'A' 162 1245
2 'B' 162 1245
3 'C' 21 417
4 'D' 21 428
5 'E' 6 6
All occupancies are one
Opening library file /usr/local/gromacs/share/top/ffgmx.atp
Atomtype 52
Reading residue database... (ffgmx)
Opening library file ffgmx.rtp
Residue 50Fatal error: Atom type OWT4 (residue HO4) not found in atomtype
database
Although there are posts to use the PRODRG, but it gives error that more
than 300 atoms cannot be processed.
i am able to do simulation the pdb without DNA.
but with protein-dna complex it shows the above error.
what may be the solution ?
Regards,
A.Raj
[EMAIL PROTECTED] wrote:
Welcome to the gmx-users@gromacs.org mailing list!
To post to this list, send your email to:
gmx-users@gromacs.org
General information about the mailing list is at:
http://www.gromacs.org/mailman/listinfo/gmx-users
If you ever want to unsubscribe or change your options (eg, switch to
or from digest mode, change your password, etc.), visit your
subscription page at:
http://www.gromacs.org/mailman/options/gmx-users/alaguraj_v%40yahoo.com
You can also make such adjustments via email by sending a message to:
[EMAIL PROTECTED]
with the word `help' in the subject or body (don't include the
quotes), and you will get back a message with instructions.
You must know your password to change your options (including changing
the password, itself) or to unsubscribe. It is:
vmsapk
Normally, Mailman will remind you of your gromacs.org mailing list
passwords once every month, although you can disable this if you
prefer. This reminder will also include instructions on how to
unsubscribe or change your account options. There is also a button on
your options page that will email your current password to you.
ALAGURAJ VELUCHAMY
c/o Dr.S.KRISHNASWAMY,
CENTRE OF EXCELLENCE IN BIOINFORMATICS,
MADURAI KAMARAJ UNIVERSITY,
MADURAI, TN.
Ph:09486148690
__________________________________________________
Shape Yahoo! in your own image. Join our Network Research Panel today!
----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
_______________________________________________
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
