Sir,
I tried clustering in ptraj and it worked ok.
When i tried to do mmpbsa.pl on the trajectory generated; snapshots
are generating but on performing pbsa and nmode calculations, pbsa
finishes giving huge negative values (7 or 9 digits) and nmode fails
to run. Problems on missing bonds errors are also in the log file.
Is there any other way to know which frames are included in each
cluster (i could create snaphots if i know the frame numbers) or
generate proper trajectory (manual says trajectory generated is in
amber format by default).?
Thanking you
mary
On 12/7/16, Mary Varughese <maryvj1985.gmail.com> wrote:
> Ok.
>
> Thank you sir
> I wil try this.
>
> On Wed, Dec 7, 2016 at 1:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>> Hi,
>>
>> This is almost right, but what you want to do is RMS-fit the DNA
>> _before_ you cluster, then cluster on your ligand using 'nofit'. So
>> something like:
>>
>> parm myparm.parm7
>> trajin mytraj.nc
>> rms first <DNA backbone mask>
>> cluster <ligand mask> nofit ...
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Thu, Dec 1, 2016 at 5:43 AM, Mary Varughese <maryvj1985.gmail.com>
>> wrote:
>> > Sir
>> >
>> > Thank you very much.
>> >
>> > This is a sample given in amber tutorial
>> >
>> > trajin traj.1.gz
>> > trajin traj.2.gz
>> > cluster out testcluster representative pdb average pdb averagelinkage
>> > clusters 5 rms .CA
>> >
>> > Is the mask part you mentioned "rms .CA" ?
>> >
>> > Are you familiar with mmtsb (i always use mmtsb as learned from amber
>> > tutorial) ? And do you know any keyword related to this?
>> >
>> > thanking you
>> >
>> > On Thu, Dec 1, 2016 at 3:56 PM, Achim Sandmann <
>> > Achim.Sandmann.chemie.stud.uni-erlangen.de> wrote:
>> >
>> >> Hello Mary Varughese,
>> >>
>> >>
>> >> So far as I understood, you want to take the ligand position with
>> >> respect to the DNA (as well as the ligand conformation itself) into
>> >> consideration.
>> >>
>> >> I think the easiest way to do this is to do a RMSD calculation with
>> >> the
>> >> DNA backbone mask first. This will align the structures. As a second
>> >> step (within the same praj/cpptraj call) you can use the cluster
>> >> command
>> >> with the mask of the ligand and the 'nofit' flag.
>> >>
>> >>
>> >> with kind regards,
>> >>
>> >> Achim Sandmann
>> >>
>> >>
>> >> Am 01.12.2016 um 08:26 schrieb Mary Varughese:
>> >> > Sir
>> >> >
>> >> > I have a DNA ligand system. After aligning all the structures with
>> >> respect
>> >> > to DNA backbone i want to cluster on the basis of ligand
>> conformation. Is
>> >> > there any way to specify that aspect in mmtsb or ptraj cluster.
>> >> >
>> >> > Thanking you
>> >> >
>> >> >
>> >> > mary varughese
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >> _______________________________________________
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>> >>
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>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://www.lobos.nih.gov/lcb
>>
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>>
>
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Received on Wed Dec 14 2016 - 03:00:03 PST
