[gmx-users] (no subject)

[Virtual Daan]

Hi

The carboxylates are likely to be deprotonated - however if you read the
PRODRG faq, you will see how you can put them back on.
I dont; understand the problem with the last (i.e. C-terminal ?) N, but
perhaps again this could be solved by taking it off and putting it back on
using the commands in the FAQ.
There will soon be a very major PRODRG update which (amongst many other
things) will address the problems associated with nitrogens in aromatic
systems.

cheers

Daan


On Mon, 14 Apr 2003,  Zhili Zuo wrote:

> hello all: I want to generate the topology for the ligand. But my
> ligand is composed of eight residues, six of them are GLU, LEU, ASP,
> VAL, GLU and PHe, and two of them are non-peptide residues in the
> middle. when I made top file in www.davapc1.bioch.dundee.ac.uk, the
> hydrogens in all the carboxyl were missing and the coordinate of
> hydrogen to the nitrogen in the last GLU is "nan".
>
> How can I generate the proper topology of my ligand?
> Thank you!!
>
>
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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O