I thought of the same and I started running it using angular mode yesterday.
Thanks though for a quick feedback.
-Vissu
On 8/11/06, David van der Spoel
<[EMAIL PROTECTED]> wrote:
Viswanadham Sridhara wrote:
> Hello everyone,
> I could figure out that parameters for NAG are not that important. So, I
> used free HEWL.
> I started running it, but I realize that the protein started to rotate
> around the center of mass with a frequency of around 200ps.
> I used "Linear" as an option for comm_mode and I used "Protein" in
> comm_grps.
> Any reason Why the protein is rotating around its center of mass, is it
> normal?
yes.
comm_mode = angular
> Thanks in advance.
> -Vissu.
>
> ---------- Forwarded message ----------
> From: *David Mobley* <[EMAIL PROTECTED] <mailto: [EMAIL PROTECTED]>>
> Date: Aug 8, 2006 12:32 AM
> Subject: Re: [gmx-users] Hen egg white lysozyme.
> To: Discussion list for GROMACS users < [email protected]
> <mailto:[email protected]>>
>
> Vissu,
>
> Depends on what you are trying to do. Many proteins deposited in the
> pdb contain "uninteresting" ligands bound to them (i.e. cosolvent
> molecules, etc.) On the other hand, sometimes ligands are functionally
> important or significantly affect the structure. You have to decide
> whether you want to include NAG or not; it might help to first figure
> out what it is and what it's used for (perhaps look up its name, and
> look at the paper and PDB headers...).
>
> It is obviously harder to come up with parameters for NAG than not. If
> you end up deciding it's not important, you can, for example, just
> remove the HETATM entries dealing with it before running pdb2gmx.
>
> David
>
>
> On 8/7/06, Viswanadham Sridhara < [EMAIL PROTECTED]
> <mailto:[EMAIL PROTECTED]>> wrote:
> > Hi Everyone,
> > I am trying to simulate a protein and I am getting the following error
> > message.
> > "NAG" not found in residue topology database. I checked gmx-users
> discussion
> > list to find out if someone ever used 1HEW.pdb . Its a hen egg-white
> > lysozyme. I did not get even a single archive about this.
> > It is under HETATM section of .pdb file. Any help is appreciated.
> > I know that I have to add this residue in aminoacids.dat file and create
> > atoms and bonds in .rtp section. Is there any other way around?
> > Thanks in advance,
> > -Vissu
> >
> > --
> > Viswanadham Sridhara,
> > Graduate Research Assistant,
> > Old Dominion University,
> > Norfolk, VA-23529.
> > _______________________________________________
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> >
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>
> --
> Viswanadham Sridhara,
> Research Assistant,
> Old Dominion University,
> Norfolk, Va-23529.
>
>
> ------------------------------------------------------------------------
>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED].
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--
Viswanadham Sridhara,
Research Assistant,
Old Dominion University,
Norfolk, Va-23529.
_______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
