Hi,
Is there any command corresponding to 'info' in ptraj ?
I am more familiarized with ptraj than cpptraj.
Thanking you
mary
On 12/15/16, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> The file written by 'out' will contain the cluster number for each frame.
> In addition, the file written by 'info' will contain parseable text
> representations of each cluster.
>
> -Dan
>
> On Wed, Dec 14, 2016 at 5:34 AM Mary Varughese <maryvj1985.gmail.com>
> wrote:
>
>> 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
>> >> >> > _______________________________________________
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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 Thu Dec 15 2016 - 02:00:02 PST
