On 5/15/12 10:43 AM, Lara Bunte wrote:
Hi
You wrote:
Two blocks of dihedrals are normal output for pdb2gmx - one for proper
and one for improper dihedrals.
Is there a way to force pdb2gmx that there is only my block with improper
dihedrals in the topology?
Normally pdb2gmx will generate proper dihedrals based on bonded connectivity.
Is there some reason to believe you should not have dihedrals? That doesn't
make much physical sense.
Could that be a problem in further calculations, i.e. energy minimization if
there is this empty [ dihedrals ] block in the topology?
What you've been defining as "empty" is not necessarily so. The fact that
parameters are not explicitly printed is not inherently indicative of a problem,
since the parameters are looked up from ffbonded.itp and not necessarily
recapitulated in the topology. If you get fatal errors about missing
parameters, that's a separate issue.
[ 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.
What would be the correct numbers in the [ bondedtypes ] for using CHARMM27
force field?
Look in charmm27.ff/aminoacids.rtp.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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