[gmx-users] Generating topology file
Hi GROMACS users, I have used acpype.py to convert parameter and topology file from amber to gromacs but some of the parameters (angle and dihedral)regarding a particular residue having mercury in it was not generating,please help. Thanks in advance. Madhumita Das -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Generating topology file
I am sorry, but because antechamber will only work with these atoms: C, N, O, S, P, H, F, Cl, Br and I, so acype won't work for Hg. A "hack" would be to replace Hg by another allowed element. But this is only to give you a hint of what topology and parameters might look like. Then you have to work hard in literature to find parameters and likely make use of RED for getting a more quantum mechanics approach for your parameters and charges. Good luck, Alan On 23 November 2011 10:35, madhumita das wrote: > Hi GROMACS users, > > I have used acpype.py to convert parameter and topology file from > amber to gromacs but some of the parameters (angle and > dihedral)regarding a particular residue having mercury in it was not > generating,please help. >Thanks > in advance. > > Madhumita Das > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Alan Wilter SOUSA da SILVA, DSc Bioinformatician, UniProt - PANDA, EMBL-EBI CB10 1SD, Hinxton, Cambridge, UK +44 1223 49 4588 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 not able to generate a topology
file of it using pdb2gmx. I tried using the The Dundee PRODRG server to
generate the topology file with the pdb file as the input. The problem is that
it does generate the topology file but without any hydrogens. Even the polar
hydrogens information is not available inspite of it being a part of my input
pdb file. Thus I am not able to use FNP with the polar hydrogens for my runs.
If anyone has faced similar problems please do help if you can.
Thanking you,
Cheers.
Soni Mufaddal Saifee,
B.Tech IIT Madras.
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[gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 hundreds of other
threads on this topic) still apply about how to come up with the parameters...
read the original papers and reproduce their methodology.
Chris.
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 not able to generate a topology file of it using pdb2gmx. I
tried using the The Dundee PRODRG server to generate the
topology file with the pdb file as the input. The problem is
that it does generate the topology file but without any
hydrogens. Even the polar hydrogens information is not
available inspite of it being a part of my input pdb file.
Thus I am not able to use FNP with the polar hydrogens for my runs.
If anyone has faced similar problems please do help if you can.
Thanking you,
Cheers.
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Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 recognize FNP and hence I am not able to
generate a topology file of it using pdb2gmx. I tried using the The
Dundee PRODRG server to generate the topology file with the pdb file
as the input. The problem is that it does generate the topology file
but without any hydrogens. Even the polar hydrogens information is
not available inspite of it being a part of my input pdb file. Thus I
am not able to use FNP with the polar hydrogens for my runs.
If anyone has faced similar problems please do help if you can.
Have you read
http://wiki.gromacs.org/index.php/Exotic_Species ?
Note however, that parametrizing some exotic molecule is a non-trivial
issue...
Good luck, Jochen
Thanking you,
Cheers.
Soni Mufaddal Saifee,
B.Tech IIT Madras.
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it now.
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Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
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RE: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
Hi Soni,
I have never had such problems, but only some suggestions:
1) Try the PRODRG beta server
(http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg_beta)
2) Try drawing your molecule (or part of it) directly with the JME
editor, included on the PRODRG website
3) Try using another input file type, 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
>Message-ID: <[EMAIL PROTECTED]>
>Content-Type: text/plain; charset="iso-8859-1"
>
>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 not
>able to generate a topology file of it using pdb2gmx. I tried using the
>The Dundee PRODRG server to generate the topology file with the pdb
>file as the input. The problem is that it does generate the topology
>file but without any hydrogens. Even the polar hydrogens information
>is not available inspite of it being a part of my input pdb file.
>Thus I am not able to use FNP with the polar hydrogens for my runs.
>
>If anyone has faced similar problems please do help if you can.
>
>Thanking you,
>Cheers.
>
>Soni Mufaddal Saifee,
>B.Tech IIT Madras.
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Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 gromacs does not recognize FNP
> and hence I am not able to generate a topology file of it using pdb2gmx. I
> tried using the The Dundee PRODRG server to generate the topology file with
> the pdb file as the input. The problem is that it does generate the topology
> file but without any hydrogens. Even the polar hydrogens information is not
> available inspite of it being a part of my input pdb file. Thus I am not able
> to use FNP with the polar hydrogens for my runs.
>
> If anyone has faced similar problems please do help if you can.
I know that PRODRG (which I believe uses the old ffgmx) does not add aromatic
hydrogens to molecules, but the PRODRG beta site (which uses GROMOS96) does.
You may want to try the beta server, since ffgmx is deprecated (as noted in the
manual).
-Justin
>
> Thanking you,
> Cheers.
>
> Soni Mufaddal Saifee,
> B.Tech IIT Madras.
>
>
> -
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it
> now.
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
[EMAIL PROTECTED] | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
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Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 Kerrigan's
tutorial.
In any case, for compounds with names like
{[7-(DIFLUORO-PHOSPHONO-METHYL)-NAPHTHALEN-2-YL]-DIFLUORO-METHYL}-PHOSPHONIC
ACID, I would scratch my head a few times and probably go search for a
different project. It's a charged fairly large, complex small molecule ;)
with everything conjugated, which makes it a daunting task to derive proper
parameters. For example, PRODRG will likely return you a naphtalene ring
with no charges, quite contrary to what you would expect, and which may be
necessary for the interaction with positive charges (a la cation-pi
interaction).
But these are just my two cEUR (which now is ~ 3 cUSD by the way ;))
Cheers,
Tsjerk
On Jan 10, 2008 7:34 PM, Chris Neale <[EMAIL PROTECTED]> wrote:
> 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 hundreds of other threads on this topic) still apply about how to come
> up with the parameters... read the original papers and reproduce their
> methodology.
>
> Chris.
>
> >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 not able to generate a topology file of it using pdb2gmx. I
> >tried using the The Dundee PRODRG server to generate the
> >topology file with the pdb file as the input. The problem is
> >that it does generate the topology file but without any
> >hydrogens. Even the polar hydrogens information is not
> >available inspite of it being a part of my input pdb file.
> >Thus I am not able to use FNP with the polar hydrogens for my runs.
> >
> >If anyone has faced similar problems please do help if you can.
> >
> >Thanking you,
> >Cheers.
>
> ___
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> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Generating topology file for a molecule (FNP) not in the gromacs library.
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 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Chris Neale wrote:
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 hundreds of other threads on this topic) still apply
about how to come up with the parameters... read the original papers and
reproduce their methodology.
Chris.
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 not able to
generate a topology file of it using pdb2gmx. I tried using the The
Dundee PRODRG server to generate the topology file with the pdb file
as the input. The problem is that it does generate the topology file
but without any hydrogens. Even the polar hydrogens information is
not available inspite of it being a part of my input pdb file. Thus I
am not able to use FNP with the polar hydrogens for my runs.
If anyone has faced similar problems please do help if you can.
Thanking you,
Cheers.
___
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