On 15/05/2012 8:47 PM, Lara Bunte wrote:
Hi
After pdb2gmx I have two [ dihedrals ] sections in my topology. The first block
is empty, the second block is correct with my parameters.
An an example:
First block:
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3 c4 c5
2 1 19 8 5
6 8 9 10 5
Second block:
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
c3
1 8 6 4 5 180 100
1 2 4 5 5 180 100
What could be the reason for this? What do I have to change in my force field
folder (CHARMM27) to fix this?
Two blocks of dihedrals are normal output for pdb2gmx - one for proper
and one for improper dihedrals.
In my .rtp file in the force field folder I have only this section for dihedrals
[ impropers ]
O4 N1 C2 N3 180 100
N1 C2 N3 H3 180 100
This produces your second block of type 5 dihedrals, given what you have
said below.
I declared my [ bondedtypes ] as the following:
[ bondedtypes ]
; bonds angles dihedrals impropers
1 1 5 5
Those are angle, dihedral and improper function types that are abnormal
for CHARMM27. Using these in your .rtp means that you are no longer
using CHARMM27. It might be reasonable for you to do this, but you need
to be absolutely sure why. Importing a topology from another force field
is not an acceptable reason.
Mark
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
