On 23/05/2012 6:42 PM, Alan wrote:
Thanks Justin, you were right. In the end gmxdump helped to clear some
doubts but I wished it would be less painfully.
One useful approach is to simplify the system as much as possible before
producing the .tpr and using gmxdump. The necessary cross-referencing is
easier to see when the complexity of the contents is low.
Mark
Cheers,
Alan
On 22 May 2012 12:36, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
On 5/22/12 12:46 PM, Alan wrote:
Hi Justin, your suggestion got close. However, let me give an
example. You can
use the Gly-Gly-Gly example I am attaching and do this:
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p aGGG.top
-water none
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o aGGG.tpr
-pp aGGGp.top
if you look at aGGGp.top I can't find which parameters were
used for
[ dihedrals ]
; ai aj ak al funct c0 c1
c2
c3 c4 c5
2 1 5 6 9
I.e., for proper dihedral (H1- N- CA- HA1), I can't find
in amber99sb.ff/forcefield.itp any combination that handles
parameters for
X-N-CA-X or X-CA-N-X, so how grompp is interpreting this dihedral?
Make sure you're looking at types, not names. The type sequence
here is H-N3-CT-HP, which I think is mapped to this dihedral:
X CT N3 X 9 0.0 0.65084 3 ; JCC,7,(1986),230
Running gmxdump on the .tpr file will show it for sure; I had
assumed it would be in the post-processed topology as well, but I
guess not.
-Justin
Thanks,
Alan
On 21 May 2012 18:50, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
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
<http://redmine.gromacs.org> <http://redmine.gromacs.org>.
-Justin
--
==============================__==========
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Virginia Tech
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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