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Kishore wrote:
Dear Mark,
As you correctly pointed out, I had looked into those improper dihedral
specifications several times before and it seems that they are properly
mentioned in the .itp file. I have been using the topologies generated
by PRODRG server for NADPH as i could not make it comply with the
inbuilt residue template library topologies. In this topologies
generated by PRODRG there is a directive called [ dihedrals ] and it
listed out all the dihedrals with comment lines showing proper and
improper dihedrals, but this seems to differ from the way the the
topologies are defined in the gromacs inbuilt template library which
only lists out the impropers. Does this make any difference in terms of
grompp interpreting them during the preprocessing? I am herein pasting a
section of that dihedrals and a snapshot of the NADPH molecule with the
atom names labelled so that you can see that the impropers you mentioned
in your reply are infact mentioned in the .itp file I am using.
Gromacs separates proper and improper dihedrals in [dihedrals] directives,
presumably for convenience. Having one or two directives with proper contents
does not make a difference. If, however, PRODRG is assigning parameters that
the force field library does not, that just sounds like typical PRODRG behavior
- its parameters are often incorrect and one has to know the proper way to
handle re-assigning parameters. Bonded parameters are often more correct than
charges and charge groups from PRODRG, which are wrong in all the cases I've
ever seen.
http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips
-Justin
The three improper dihedrals you have mentioned are highlighted
below...please correct me in case if i am getting the meaning
wrong..Sorry for flooding with long posts, but I am in a great need for
some help on this.
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
1 4 3 2 2 0.0 167.4 0.0 167.4 ; imp NBS
CBQ H8M HBS
4 1 5 6 2 0.0 167.4 0.0 167.4 ; imp CBQ
NBS OBT CAV
6 4 9 7 2 0.0 167.4 0.0 167.4 ; imp CAV
CBQ CBE CAN
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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