The actual parameters are listed in the ffbonded.itp file located in the
folder of the corresponding force field, under [ dihedraltypes ] section.
Javier
El 21/05/12 14:43, Alan escribió:
Hi there,
Is there an option in pdb2gmx that when generating the top/itp file,
it could show the parameters explicitly? e.g.:
Instead of:
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
5 13 11 12 4
11 15 13 14 4
15 23 21 22 4
21 25 23 24 4
25 32 31 33 4
(my hard hand modifications)
[ dihedrals ] ; impropers
; treated as propers in GROMACS to use correct AMBER analytical function
; i j k l func phase kd pn
5 13 11 12 4 180.00 43.93200 2 ; CA-
N- C- O
11 15 13 14 4 180.00 4.60240 2 ; C-
CA- N- H
15 23 21 22 4 180.00 43.93200 2 ; CA-
N- C- O
21 25 23 24 4 180.00 4.60240 2 ; C-
CA- N- H
25 32 31 33 4 180.00 43.93200 2 ; CA-
OC1- C- OC2
I mean, if the parameters that are hiding in e.g.
...gromacs/top/amber99sb.ff could be showed in the top/itp file for
human readers, that would be great.
Thanks,
Alan
--
Alan Wilter SOUSA da SILVA, DSc
Bioinformatician, UniProt - PANDA, EMBL-EBI
CB10 1SD, Hinxton, Cambridge, UK
+44 1223 49 4588
--
Javier CEREZO BASTIDA
PhD Student
Physical Chemistry
Universidad de Murcia
Murcia (Spain)
Tel: (+34)868887434
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