PyMOL + AMBER Trajectories

From: DeLano, Warren <warren_at_sunesis.com>
Date: Thu 29 Aug 2002 11:27:01 -0700

Amber users,

I am working on a development version of PyMOL which can read amber topology and trajectory files directly for one-stop visualization and ray-tracing. This is new code (not based on ptraj) and it supports use of PyMOL's selection language to pull-out the sub-regions of the trajectory on-the-fly (no preprocessing required!).

It also supports averaging during the read and it allows you pull-out specific segments (with skipping, if desired). You can also string trajectories together, so long as they are based on the same topology file.

Before releasing this new version, I'd like to get my hands on a representative set of topology/trajectory pairs from a variety of diverse sources in order to make sure that it actually works for "real-world" systems.

If you would like to help and are willing to share some small non-confidential/non-proprietary trajectory files (with matching topology files, required), then respond directly to me (warren_at_sunesis.com) and I'll send you an FTP login where you can upload your test case.

For the sake of practicality, let's limit this to trajectory files less 100 MB (the smaller the better), with an emphasis on unusual stuff.

Thanks,
Warren

--
mailto:warren_at_sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606  FAX:(650)-266-3501
> -----Original Message-----
> From: Carlos Simmerling [mailto:carlos.simmerling_at_sunysb.edu]
> Sent: Wednesday, August 28, 2002 10:10 AM
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: Fw: amber problem
> 
> 
> 
> 
> I am forwarding this to the AMBER mailing list.
> That is where you should send these questions, so
> all AMBER users can try to help.
> Carlos
> 
> >            Dr. Bill told me that I should read the FAQ about
> > equilibration.  And I searched some input template in the 
> netscape, and
> > found a simulated annealing could solve my problem, the 
> sander does not
> > stop. But in the output file, it always says that  "vlimit 
> exceeded for
> > step  *; vmax =   39.8214423", or something like that. So I 
> wonder if it
> > would influence my results.
> >             Another question about sander is, I am confused 
> about when I
> > should use  the ntb=1, and ntb=2. My protein is soaked in a 
> cubic water
> > box. To make PBC work, which parameter should I use. My new 
> input file
> > is the following, I have changed some parameters, I wish 
> you could tell
> > me if there are something wrong in it.
> >             Thank you very much for your advice.
> > 
> > --------------------------------
> >    &cntrl
> >     nstlim=20000,
> >     ntpr=200, ntt=1, ntwx=200,
> >     ntb=1, vlimit=20,scee=1.2,
> >  &end
> >  &ewald
> >     eedmeth=5,
> >  &end
> > #
> > #Simple simulated annealing algorithm:
> > #
> > #from steps 0 to 5000: heat the system to 600K
> > #from steps 5001-18000: re-cool to low temperatures with long tautp
> > #from steps 18001-20000: final cooling with short tautp
> > #
> >  &wt type='TEMP0', istep1=0,istep2=5000,value1=600.,
> >             value2=600.,    &end
> >  &wt type='TEMP0', istep1=5001, istep2=18000, value1=600.0,
> >             value2=100.0,     &end
> >  &wt type='TEMP0', istep1=18001, istep2=20000, value1=0.0,
> >             value2=0.0,     &end
> > 
> >  &wt type='TAUTP', istep1=0,istep2=5000,value1=0.4,
> >             value2=0.4,     &end
> >  &wt type='TAUTP', istep1=5001,istep2=18000,value1=4.0,
> >             value2=4.0,     &end
> >  &wt type='TAUTP', istep1=18001,istep2=19000,value1=1.0,
> >             value2=1.0,     &end
> >  &wt type='TAUTP', istep1=19001,istep2=20000,value1=0.1,
> >             value2=0.05,    &end
> > 
> >  &wt type='REST', istep1=0,istep2=3000,value1=0.1,
> >             value2=1.0,  &end
> >  &wt type='REST', istep1=3001,istep2=20000,value1=1.0,
> >             value2=1.0,  &end
> > 
> >  &wt type='END'  &end
> > --------------------------------
> > 
> > 
> 
> 

Received on Thu Aug 29 2002 - 11:27:01 PDT