foh wrote:
Thanks you.
But, that it is necessary to write in 4 column for simple molecules of type
methane, ethane
for OPLS potential ?
HEADER METHANE
ATOM 1 CB ??? 1 3.875 0.678 -8.417 1.00 0.00
ATOM 2 HB1 ??? 1 3.800 1.690 -8.076 1.00 0.00
ATOM 3 HB2 ??? 1 4.907 0.410 -8.516 1.00 0.00
ATOM 4 HB3 ??? 1 3.406 0.026 -7.711 1.00 0.00
ATOM 5 HB4 ??? 1 3.389 0.583 -9.366 1.00 0.00
END
I can't understand your question. The point of pdb2gmx is to take a
structure and a forcefield, look up its topology in the database, and to
write a consistent .top file (see
http://wiki.gromacs.org/index.php/.top_file). It only makes sense to
give it a structure that has a topology that is in its database - and
not all structures are, obviously.
Read chapter 5 of the manual, read ffoplsaa.rtp and find out whether you
need to write your .top by hand.
You should also do some tutorial material to get your brain around the
usual gromacs way of doing things, before you try to work out how to do
whatever you want to do on the system you're interested in.
Mark
_______________________________________________
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
