RE: question on residue rmsd.tcl

From: Ada Zhan (zyqfrog10_at_msn.com)
Date: Mon Jun 06 2011 - 14:25:36 CDT

Hi, Amit,

> actually I wanted to know whether residue_rmsd.tcl script runs for both water sphere and water box based generated trajectories
 As I said, residue_rmsd.tcl only selects protein residue atoms, so it is independent of water box shape.

> Could you please help me out with the distance.tcl script. I was not able to run the default script provided with the tutorial.
 I would like to help. But it is hard to help if you don't clarify your procedure and what error message(s) you get. You know, there are many reasons for a script not working. Sometimes, small carelessness is not detectable.
I would suggest you follow the tutorial instruction step by step and do it over again.
If it is still not working, I would suggest you ask some experienced individual around you (your supervisor or your college) to watch through how you follow the tutorial and help you identify where you make mistake.

Good luck!

Ada
Date: Sun, 5 Jun 2011 22:18:48 -0700
From: amit_informatics_at_yahoo.com
Subject: Re: namd-l: question on residue rmsd.tcl
To: zyqfrog10_at_msn.com; namd-l_at_ks.uiuc.edu

Dear Ada,
Thanks for your reply, actually I wanted to know whether residue_rmsd.tcl script runs for both water sphere and water box based generated trajectories.
Could you please help me out with the distance.tcl script. I was not able to run the default script provided with the tutorial.

Thanks and Regards,
Amit
From: Ada Zhan <zyqfrog10_at_msn.com>
To: amit_informatics_at_yahoo.com; namd-l_at_ks.uiuc.edu
Sent: Fri, June
 3, 2011 12:36:00 AM
Subject: RE: namd-l: question on residue rmsd.tcl

Him Amit,

residue_rmsd.tcl runs for protein. It does nothing to do with water.

Best,
Ada

Date: Wed, 1 Jun 2011 20:49:17 -0700
From: amit_informatics_at_yahoo.com
Subject: namd-l: question on residue rmsd.tcl
To: namd-l_at_ks.uiuc.edu

 
Dear colleagues,
                         Please let me know whether residue_rmsd.tcl script will run for water sphere trajectories? Becuase in the NAMD tutorial it is given for water box models.
 
Yours truly,
Amit
                                               

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