I had exactly the same question to ask the users. I hope someone would give a better idea to generate gro and itp for a polymer of your choice molecular weight.
Currently, what I am doing is to create a smaller polymer using prodrg and manually extend the itp to the size I want. I know this is not the best way, however, since polymer topology has just same pattern, its easy to create the itp file.
However, to extend the gro file, we need to use the angle information and may be write a script.
I don't know if this a good idea??
Mohan
On 08/11/06,
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Today's Topics:
1. Re: Creation of an index file with seperate lipid leaflets
(Jay Mashl)
2. Re: pdb2gmx and protein DNA complexes (Erik Marklund)
3. Re: pdb2gmx and protein DNA complexes (Erik Marklund)
4. How to generate GRO and TOP file for high-number-atom
polymer? (WU Yanbin)
5. What if the atom number exceed 99999 for Gromacs file? (WU Yanbin)
----------------------------------------------------------------------
Message: 1
Date: Wed, 8 Nov 2006 11:32:20 -0600 (CST)
From: Jay Mashl <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Creation of an index file with seperate lipid
leaflets
To: Discussion list for GROMACS users <[email protected]>
Message-ID:
<[EMAIL PROTECTED] >
Content-Type: TEXT/PLAIN; charset=US-ASCII
Wasted work would be bad ;)
Rather than headgroup orientation, maybe try looking at atom distributions
along the bilayer normal direction. Neutron scattering experiments show that
for atom groups far from the bilayer midplane, the corresponding z-coordinates
form two distinct distributions. So one way could be the following. Pick a
headgroup atom and obtain its z-coordinate. Have make_ndx accept this value as
input. Search the system by looping over lipids and ask whether that atom type
has a z-coordinate within some amount around the input value. From this you
know the membership of the leaflets. A more automatic way would be to have the
program first discern the distribution and then reread the system to decide the
leaflet membership.
Jay
On Wed, 8 Nov 2006, Alan Dodd wrote:
> Wouldn't shuffle/sort undo all the good work? I did
> wonder if I should have labelled the lipids in
> different leaflets as different molecule types, or
> different chains, but it's a bit late now...
>
> --- Jay Mashl < [EMAIL PROTECTED]> wrote:
>
> > On Wed, 8 Nov 2006, Alan Dodd wrote:
> > > Has anyone already created a way to generate an
> > index
> > > file with the atoms from the two leaflets of a
> > bilayer
> > > listed seperately? I can't believe it hasn't
> > already
> > > been done, but can't find a direct description of
> > a
> > > solution. I'm attempting a modification to
> > make_ndx,
> > > (or perhaps something considerably less ambitious,
> > > judging by the way it's going so far) to permit
> > lipid
> > > selection based on headgroup orientation, though
> > I'd
> > > quite like to save myself the effort.
> > > Incidentally, splitres and splitat seem to be the
> > > wrong way around, unless I'm misunderstanding them
> > -
> > > they do the opposite of what they say. From the
> > > gromacs 3.3.1 source download I did on April of
> > this
> > > year.
> >
> > Reordering the lipids into leaflets in your starting
> > coordinate
> > file might be a good idea. If you anticipate lipid
> > exchange between leaflets,
> > then a more general tool like what you suggest would
> > be helpful.
> >
> > Jay
> >
> > _______________________________________________
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> >
>
>
>
>
>
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------------------------------
Message: 2
Date: Wed, 8 Nov 2006 18:44:24 +0100
From: "Erik Marklund" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
To: "Discussion list for GROMACS users" < [email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the manual.
/Erik
----- Original Message -----
From: Debojyoti Dutta
To: [email protected]
Sent: Wednesday, November 08, 2006 6:08 PM
Subject: [gmx-users] pdb2gmx and protein DNA complexes
Hi
I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.
Program pdb2gmx, VERSION 3.3
Source code file: resall.c , line: 438
Fatal error:
Residue 'C' not found in residue topology database
The pdb segment is as follows:
ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 N
ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 N
Has anyone encountered this problem before?
Regards
Debo
--
---------------------------------------------
Debojyoti Dutta, PhD (USC)
http://catarina.usc.edu/~ddutta
---------------------------------------------
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Message: 3
Date: Wed, 8 Nov 2006 18:49:49 +0100
From: "Erik Marklund" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
To: "Discussion list for GROMACS users" <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
...and not just the atoms. Make sure that the residue names are the correct ones for your forcefield. Apparently, the forcefield you're using does not have a 'C'-residue.
/Erik
----- Original Message -----
From: Erik Marklund
To: Discussion list for GROMACS users
Sent: Wednesday, November 08, 2006 6:44 PM
Subject: Re: [gmx-users] pdb2gmx and protein DNA complexes
Yes, very recently actually. What forcefield are you using? If you're using the AMBERXX-port, you might want to have a look at http://folding.stanford.edu/ffamber/. Regardless of your ff, make sure that the atoms in your pdb match the ones in ff[your_forcefield].rtp. Oh, and read the manual.
/Erik
----- Original Message -----
From: Debojyoti Dutta
To: [email protected]
Sent: Wednesday, November 08, 2006 6:08 PM
Subject: [gmx-users] pdb2gmx and protein DNA complexes
Hi
I am trying to simulate a protein DNA complex but I am stuck at the pdb2gmx stage as it gets stuck when it encounters a nucleotide.
Program pdb2gmx, VERSION 3.3
Source code file: resall.c, line: 438
Fatal error:
Residue 'C' not found in residue topology database
The pdb segment is as follows:
ATOM 1239 NZ LYS B 513 -24.159 16.372 -25.774 1.00 51.42 N
ATOM 1249 N1 C C 1 - 10.253 8.018 40.704 1.00 25.86 N
Has anyone encountered this problem before?
Regards
Debo
--
---------------------------------------------
Debojyoti Dutta, PhD (USC)
http://catarina.usc.edu/~ddutta
---------------------------------------------
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Message: 4
Date: Wed, 8 Nov 2006 16:32:11 -0600
From: "WU Yanbin" <[EMAIL PROTECTED]>
Subject: [gmx-users] How to generate GRO and TOP file for
high-number-atom polymer?
To: [email protected]
Message-ID:
<[EMAIL PROTECTED] >
Content-Type: text/plain; charset="iso-8859-1"
Hi,
Genearlly I generate GRO and TOP file for polymer using PRODRG. But
PRODRG does not work when the atom number of the polymer exceeds 300. So can
anyone recommend other software and method? Thanks.
Yours Sincerely,
WU Yanbin
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Message: 5
Date: Wed, 8 Nov 2006 18:11:42 -0600
From: "WU Yanbin" < [EMAIL PROTECTED]>
Subject: [gmx-users] What if the atom number exceed 99999 for Gromacs
file?
To: [email protected]
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I built up a box of polymer with box size 20x20x20 and then solvate the
box with water using Genbox. Thus the total atom number exceeds 99999 and I
found that the atom number starts from zero when it exceeds 99999. Does it
matter for the ongoing command "grompp" and "mdrun"? Thanks.
Yours Sincerely,
WU Yanbin
--
-----------------------------------------------------------------------------------------------------------------------
WU Yanbin
Department of Mechanical Science and Engineering Email:
[EMAIL PROTECTED]
3323 Beckman Institute
Phone: (217)819-9064
University of Illinois at Urbana-Champaign
405 N. Mathews Avenue
Urbana, IL 61801
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