VMD-L Mailing List

From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Tue Feb 15 2005 - 20:29:32 CST

Ohhh....

Well, the CHARMM parameter name for a protonated ASP is ASPP...
However, the name of your residue will not change unless you apply an alias or
pdbalias command.

The fact that your residue is an ASP should do your job more easy, because all
you have to do is save a hydrogen-less version of your file and build a new
psf file without the patch part.

That should do the trick....

Luis.

PS: The list appears to be deserted....

---------- Original Message -----------
From: Gaurav Sharma <sharma_at_coe.neu.edu>
To: Luis Rosales <ludwig_at_correo.biomedicas.unam.mx>
Cc: vmd-l_at_ks.uiuc.edu
Sent: Tue, 15 Feb 2005 18:13:16 -0500
Subject: Re: vmd-l: Unprotonating GLU, ASP

> Hi Ludwig,
>
> I used the following commands to protonate the D residues:
>
> segment A { pdb gcn4A.pdb }
> patch ASPP A:7
> coordpdb gcn4A.pdb A
> guesscoord
> writepsf ....
> writepdb ....
>
>
> Are you sure the residue name changes after applying patch command ?
>
> Regards,
> Gaurav
>