Re:

From: Michael Grabe (mgrabe_at_itsa.ucsf.edu)
Date: Fri Apr 08 2005 - 12:31:36 CDT

Hello Michel,

So I am very particular about the placement of my
initial hydrogens. This is why I use Modeller with the
hydrogens turned on. I want to preserve the exact
positions of all of the hydrogens when creating
my initial PDB/PSF file using psfgen.

Thanks,
Michael

On Apr 8, 2005, at 10:27 AM, Michel Espinoza-Fonseca wrote:

> Hi Michael,
>
> I guess what you have to do is very easy. First of all, remove all
> hydrogens from your protein using Swiss PDB viewer, for example. Then
> save your pdb file WITHOUT hydrogens. After that, use the pdb file
> without hydrogens to create your pdb and psf files, using psfgen
> (psfgen will add the hydrogens automatically).
>
> If you have further questions, make me know…
>
> I hope it helps,
>
> Peace,
>
> Michel
>
>  
>
>
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Michael Grabe
> Sent: Friday, April 08, 2005 12:05 PM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l:
>
>  
>
> hello all,
>
>  
>
> i use modeller to produce homology models with hydrogen atoms,
>
> and it seems that the naming convention for the hydrogens
>
> is different from the naming convention used inthe CHARMM files
>
> I use to create the topology files. I use psfgen for this step.
>
> I have tried to use the alias command for some of these but that
>
> is a lot of hydrogens.
>
>  
>
> has some one compiled all of the correct aliases for the conversion
>
> between these two formats?
>
>  
>
> thanks
>
> michael
>
>
> -----------------------------------------------------------------------
> ---------------------------
>
> Michael Grabe, Ph.D.
>
> HHMI/UCSF
>
> Genetics Development & Behavioral Science Building
>
> 1550 4th Street, GD 481
>
> San Francisco, CA 94143-0725
>
> tel: ++ 415.476.0421
>
> http://itsa.ucsf.edu/~mgrabe
>
>  
>
------------------------------------------------------------------------
--------------------------
Michael Grabe, Ph.D.
HHMI/UCSF
Genetics Development & Behavioral Science Building
1550 4th Street, GD 481
San Francisco, CA 94143-0725
tel: ++ 415.476.0421
http://itsa.ucsf.edu/~mgrabe

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