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On 23/05/2012 6:42 PM, Alan wrote:
<blockquote
cite="mid:CAEznbzmHrweAcvyZj2YVLebi-JGXHic1Pqr3fq9CMfuuj4XRDg@mail.gmail.com"
type="cite">Thanks Justin, you were right. In the end gmxdump
helped to clear some doubts but I wished it would be less
painfully.</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEznbzmHrweAcvyZj2YVLebi-JGXHic1Pqr3fq9CMfuuj4XRDg@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Alan<br>
<br>
<div class="gmail_quote">On 22 May 2012 12:36, Justin A. Lemkul
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im"><br>
<br>
On 5/22/12 12:46 PM, Alan wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Justin, your suggestion got close. However, let me
give an example. You can<br>
use the Gly-Gly-Gly example I am attaching and do this:<br>
<br>
pdb2gmx -ff amber99sb -f aGGG.pdb -o aGGG_.pdb -p
aGGG.top -water none<br>
/sw/bin/grompp -c aGGG_.pdb -p aGGG.top -f SPE.mdp -o
aGGG.tpr -pp aGGGp.top<br>
<br>
if you look at aGGGp.top I can't find which parameters
were used for<br>
<br>
[ dihedrals ]<br>
; ai aj ak al funct c0
c1 c2<br>
c3 c4 c5<br>
2 1 5 6 9<br>
<br>
I.e., for proper dihedral (H1- N- CA- HA1), I
can't find<br>
in amber99sb.ff/forcefield.itp any combination that
handles parameters for<br>
X-N-CA-X or X-CA-N-X, so how grompp is interpreting this
dihedral?<br>
<br>
</blockquote>
<br>
</div>
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:<br>
<br>
X CT N3 X 9 0.0 0.65084 3 ;
JCC,7,(1986),230<br>
<br>
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.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="im">
Thanks,<br>
<br>
Alan<br>
<br>
On 21 May 2012 18:50, Justin A. Lemkul <<a
moz-do-not-send="true" href="mailto:jalemkul@vt.edu"
target="_blank">jalemkul@vt.edu</a><br>
</div>
<div>
<div class="h5">
<mailto:<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>>
wrote:<br>
<br>
<br>
<br>
On 5/21/12 2:43 PM, Alan wrote:<br>
<br>
Hi there,<br>
<br>
Is there an option in pdb2gmx that when
generating the top/itp file, it<br>
could<br>
show the parameters explicitly? e.g.:<br>
<br>
Instead of:<br>
[ dihedrals ]<br>
; ai aj ak al funct c0
c1 c2<br>
c3<br>
5 13 11 12 4<br>
11 15 13 14 4<br>
15 23 21 22 4<br>
21 25 23 24 4<br>
25 32 31 33 4<br>
<br>
(my hard hand modifications)<br>
<br>
[ dihedrals ] ; impropers<br>
; treated as propers in GROMACS to use correct
AMBER analytical function<br>
; i j k l func phase
kd pn<br>
5 13 11 12 4 180.00
43.93200 2 ; CA- N-<br>
C- O<br>
11 15 13 14 4 180.00
4.60240 2 ; C- CA-<br>
N- H<br>
15 23 21 22 4 180.00
43.93200 2 ; CA- N-<br>
C- O<br>
21 25 23 24 4 180.00
4.60240 2 ; C- CA-<br>
N- H<br>
25 32 31 33 4 180.00
43.93200 2 ; CA- OC1-<br>
C- OC2<br>
<br>
I mean, if the parameters that are hiding in
e.g.<br>
...gromacs/top/amber99sb.ff<br>
could be showed in the top/itp file for human
readers, that would be great.<br>
<br>
<br>
You can obtain these parameters (I believe) by
running grompp with the -pp<br>
option. If you think it would be a useful feature
for pdb2gmx, file a<br>
</div>
</div>
feature request on <a moz-do-not-send="true"
href="http://redmine.gromacs.org" target="_blank">redmine.gromacs.org</a>
<<a moz-do-not-send="true"
href="http://redmine.gromacs.org" target="_blank">http://redmine.gromacs.org</a>>.<br>
<br>
-Justin<br>
<br>
--<br>
==============================__==========
<div class="im"><br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
</div>
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--<br>
Alan Wilter SOUSA da SILVA, DSc<br>
Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
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</blockquote>
<div class="HOEnZb">
<div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true"
href="http://vt.edu" target="_blank">vt.edu</a> |
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-- <br>
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<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>
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