CHARMM partial charges and paratool

From: Jose R. Sabino (jrsabino_at_gmail.com)
Date: Fri Aug 03 2007 - 16:48:55 CDT

Hi all,

I was wondering if someone out there who is experienced with model compound
parametrization, could tell me how should one define the system+water
gaussian calculations for the charmm FF charges determination. Is it one per
one molecule? I can't figure it out. Besides, does someone knows of an
extended user guide to paratool?

thanks in advance,

Jose

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Shulin Zhuang" <shulin.zhuang_at_gmail.com>
Cc: <namd-l_at_ks.uiuc.edu>; <vmd-l_at_ks.uiuc.edu>
Sent: Friday, August 03, 2007 12:58 PM
Subject: namd-l: Re: vmd-l: How to calculate the C alpha RMSD from NAMD
trajectory

>
> Hi,
>
> On Fri, Aug 03, 2007 at 03:31:22PM +0800, Shulin Zhuang wrote:
>> I just do a MD simulations of a small protein using NAMD soft, now, I
>> want
>> to calculate the C alpha RMSD of the protein from the trajectory. Using
>> VMD,
>> only the backbone RMSD can be calculated.
>
> Please see the VMD tutorials and the User's Guide.
> You can make arbitrary atom selections for which RMSD can be calculated.
>
>> Another question:
>> For hydrogen analysis, how to calculate the hydrogen bond like soft
>> PTRAJ.
>> PTRAJ can easily calculate many kind of RMSD from Amber or charmm
>> trajectory. How can we use ptraj to analyze trajectory produced by
>> NAMD.
>
> You could use CatDCD or VMD to convert a NAMD DCD trajectory into a format
> supported by PTRAJ, that's the best thing that comes to mind. You might
> check
> to see if PTRAJ already supports DCD files, it might do so already.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>
>
> --
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>

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