Chris
This is, what I usually do, too.
Still you need the parameters for your ligand from somewhere ;)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2
Hi,
Contrary to Chris, I think it's easier/better to leave the .rtp database for
building blocks of chains (and definitely advocate against bothering with
the file for newbies). Small ligand topologies are better made seperately
"by hand" and inserted in manner similar to the procedure in John Ker
When actually building the topology I find it easiest to create the residues in
the relevant .rtp and allow pdb2gmx to build the topology for you. However, all
this does is correctly connect everything and put your parameters where they
should be. All previous comments (in this thread and the h
, e.g. MDL MOLfile
Hope it helps,
Jeroen
>Date: Thu, 10 Jan 2008 02:48:46 -0800 (PST)
>From: Mufaddal Soni <[EMAIL PROTECTED]>
>Subject: [gmx-users] Generating topology file for a molecule (FNP) not
> in the gromacs library.
>To: gmx-users@gromacs.org
>Messa
Mufaddal Soni wrote:
Dear users,
I am working with PTP1B protein. Recently I tried to
run it in gromacs along with an inhibitor
{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID[FNP in short]. The problem
is that gromacs does not recogniz
Quoting Mufaddal Soni <[EMAIL PROTECTED]>:
> Dear users,
> I am working with PTP1B protein. Recently I tried to run it
> in gromacs along with an inhibitor
> {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN- 2-YL]-DIFLUORO-METHYL}-PHOSPHONIC
> ACID[FNP in short]. The problem is that
Dear users,
I am working with PTP1B protein. Recently I tried to run it in
gromacs along with an inhibitor {[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-
2-YL]-DIFLUORO-METHYL}-PHOSPHONIC ACID[FNP in short]. The problem is that
gromacs does not recognize FNP and hence I am no
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