On 5/21/12 2:43 PM, Alan wrote:
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.
You can obtain these parameters (I believe) by running grompp with the -pp
option. If you think it would be a useful feature for pdb2gmx, file a feature
request on redmine.gromacs.org.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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