Re: [gmx-users] special molecule
Does it mean, that the itp file, generated by the PRODRG server should only used with the gmx forcefield, or may it be combined with the other gromos frocefields, like the G43a2?On 6/13/06, Mark Abraham <[EMAIL PROTECTED]> wrote: Dongsheng Zhang wrote:> Sear Mark,>> Since PRODRG server only generates a itp file by using gromos type force> field, do I have to use gromos force field for my whole protein-ligand> system if my ligand force field parameters are got from PRODRG? In > another word, can I mix two different force field (one for protein, one> for ligand) in one system? Thanks!It's technically possible, if fiddly, but I'd strongly advise againstit. Force fields are mathematical constructs that are optimized to produce reasonable model physics as an interacting unit. There is noreason to suppose that a bond stretching parameter is a measure of bondstrength, for example, because the other parameters in this force field might have some quirk that this parameter is compensating for because ofthe optimization procedure. A force field is merely a point in ahigh-dimensional space which when used the right way has been shown to produce a useful physical model. Thus there is no reason to suppose thata few of those high-dimensional space coordinates plus some others fromsome other force field will combine to produce a useful physical model. Mark___gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] .Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
What I asked is, if I have to reorganise the pdb file, or renumber the residues, etc.On 6/13/06, Mark Abraham < [EMAIL PROTECTED]> wrote:Tamas Horvath wrote:> So if I generate an .itp with PRODRG, and link it in the .top file, then > grompp can use the original .pdb file? Or it's not that simple?The order of the [ molecules ] section will have to correspond to theorder in the structure file you supply with -c to grompp, but if you read the grompp manpage it is obvious that the format of that structurefile is irrelevant.Mark___gmx-users mailing list gmx-users@gromacs.orghttp://www.gromacs.org/mailman/listinfo/gmx-usersPlease don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED].Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
Dongsheng Zhang wrote: Sear Mark, Since PRODRG server only generates a itp file by using gromos type force field, do I have to use gromos force field for my whole protein-ligand system if my ligand force field parameters are got from PRODRG? In another word, can I mix two different force field (one for protein, one for ligand) in one system? Thanks! It's technically possible, if fiddly, but I'd strongly advise against it. Force fields are mathematical constructs that are optimized to produce reasonable model physics as an interacting unit. There is no reason to suppose that a bond stretching parameter is a measure of bond strength, for example, because the other parameters in this force field might have some quirk that this parameter is compensating for because of the optimization procedure. A force field is merely a point in a high-dimensional space which when used the right way has been shown to produce a useful physical model. Thus there is no reason to suppose that a few of those high-dimensional space coordinates plus some others from some other force field will combine to produce a useful physical model. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
Tamas Horvath wrote: So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple? The order of the [ molecules ] section will have to correspond to the order in the structure file you supply with -c to grompp, but if you read the grompp manpage it is obvious that the format of that structure file is irrelevant. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] special molecule
Hi,
On Monday 12 June 2006 17:25, Dongsheng Zhang wrote:
> Sear Mark,
>
> Since PRODRG server only generates a itp file by using gromos type force
> field, do I have to use gromos force field for my whole protein-ligand
> system if my ligand force field parameters are got from PRODRG? In
> another word, can I mix two different force field (one for protein, one
> for ligand) in one system? Thanks!
Mixing ff types is a bad idea, i don`t know if PRODRG supports other ff like
the old and depracted gmx format.
I hope that there will be soon a PRODRG version which will support other force
field formats, also amber ff in gromacs without heavy modifing the pdb file.
As a hint: Take a look at
http://www.gromacs.org/gromacs/documentation/tutorial.html
for builing a system of ligand and protein.
>
>
> Best Wishes!
>
> Dongsheng
>
> On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham wrote:
> > Tamas Horvath wrote:
> > > As I understand, if there are "special" molecules in a pdb file,
> > > pdb2gmx cannot convert it. However, PRODRG can create an *.itp file for
> > > that molecule, so that I can include it in the generated topology file.
> > > But how can I place the molecule in it's original position? Or even
> > > better, how can I convert the original ("full") .pdb file for gromacs?
> >
> > Where's the problem? pdb2gmx makes a .top file for your non-special
> > system, you #include the .itp file for your special part. There's
> > nothing about atomic positions yet have a look at a .top file. Now
> > grompp takes the .top and some file with atomic positions and makes a
> > .tpr file. Same general procedure as normal.
> >
> > Mark
> > ___
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Greetings,
Florian
--
---
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Computer-Chemie-Centrum
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D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
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Re: [gmx-users] special molecule
So if I generate an .itp with PRODRG, and link it in the .top file, then grompp can use the original .pdb file? Or it's not that simple?On 6/12/06, Alan Dodd
<[EMAIL PROTECTED]> wrote:It's entirely possible to mix and match forcefield
files to create a hybrid forcefield - the lipidforcefield I use has OPLS parameters for theheadgroups, custom parameters for lipid tails, and GMXparameters for everything else. As long as the hybridforcefield is internally consistent, it will work.
How accurate it is, is another matter...So yes, you can technically use PRODRG itps with otherforcefields, but bear in mind firstly, atomtypes etcin your itp file will all need checking to make surethey are accounted for in both forcefields (are
'default' values the same in one forcefield asanother, for instance? Probably not - you may need toalter the itp to describe defaults explicitly), andsecondly that they are not designed to be used in the
same system.--- Dongsheng Zhang <[EMAIL PROTECTED]>wrote:> Sear Mark,>> Since PRODRG server only generates a itp file by
> using gromos type force> field, do I have to use gromos force field for my> whole protein-ligand> system if my ligand force field parameters are got> from PRODRG? In> another word, can I mix two different force field
> (one for protein, one> for ligand) in one system? Thanks!>>> Best Wishes!>> Dongsheng On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham> wrote:
> > Tamas Horvath wrote:> > > As I understand, if there are "special"> molecules in a pdb file, pdb2gmx> > > cannot convert it. However, PRODRG can create an> *.itp file for that
> > > molecule, so that I can include it in the> generated topology file. But> > > how can I place the molecule in it's original> position? Or even better,> > > how can I convert the original ("full") .pdb
> file for gromacs?> >> > Where's the problem? pdb2gmx makes a .top file for> your non-special> > system, you #include the .itp file for your> special part. There's> > nothing about atomic positions yet have a look
> at a .top file. Now> > grompp takes the .top and some file with atomic> positions and makes a> > .tpr file. Same general procedure as normal.> >> > Mark> > ___
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Re: [gmx-users] special molecule
It's entirely possible to mix and match forcefield
files to create a hybrid forcefield - the lipid
forcefield I use has OPLS parameters for the
headgroups, custom parameters for lipid tails, and GMX
parameters for everything else. As long as the hybrid
forcefield is internally consistent, it will work.
How accurate it is, is another matter...
So yes, you can technically use PRODRG itps with other
forcefields, but bear in mind firstly, atomtypes etc
in your itp file will all need checking to make sure
they are accounted for in both forcefields (are
'default' values the same in one forcefield as
another, for instance? Probably not - you may need to
alter the itp to describe defaults explicitly), and
secondly that they are not designed to be used in the
same system.
--- Dongsheng Zhang <[EMAIL PROTECTED]>
wrote:
> Sear Mark,
>
> Since PRODRG server only generates a itp file by
> using gromos type force
> field, do I have to use gromos force field for my
> whole protein-ligand
> system if my ligand force field parameters are got
> from PRODRG? In
> another word, can I mix two different force field
> (one for protein, one
> for ligand) in one system? Thanks!
>
>
> Best Wishes!
>
> Dongsheng
>
>
>
> On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham
> wrote:
> > Tamas Horvath wrote:
> > > As I understand, if there are "special"
> molecules in a pdb file, pdb2gmx
> > > cannot convert it. However, PRODRG can create an
> *.itp file for that
> > > molecule, so that I can include it in the
> generated topology file. But
> > > how can I place the molecule in it's original
> position? Or even better,
> > > how can I convert the original ("full") .pdb
> file for gromacs?
> >
> > Where's the problem? pdb2gmx makes a .top file for
> your non-special
> > system, you #include the .itp file for your
> special part. There's
> > nothing about atomic positions yet have a look
> at a .top file. Now
> > grompp takes the .top and some file with atomic
> positions and makes a
> > .tpr file. Same general procedure as normal.
> >
> > Mark
> > ___
> > gmx-users mailing listgmx-users@gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> list. Use the
> > www interface or send it to
> [EMAIL PROTECTED]
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> http://www.gromacs.org/mailing_lists/users.php
> ___
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Re: [gmx-users] special molecule
Sear Mark,
Since PRODRG server only generates a itp file by using gromos type force
field, do I have to use gromos force field for my whole protein-ligand
system if my ligand force field parameters are got from PRODRG? In
another word, can I mix two different force field (one for protein, one
for ligand) in one system? Thanks!
Best Wishes!
Dongsheng
On Tue, 2006-06-13 at 01:16 +1000, Mark Abraham wrote:
> Tamas Horvath wrote:
> > As I understand, if there are "special" molecules in a pdb file, pdb2gmx
> > cannot convert it. However, PRODRG can create an *.itp file for that
> > molecule, so that I can include it in the generated topology file. But
> > how can I place the molecule in it's original position? Or even better,
> > how can I convert the original ("full") .pdb file for gromacs?
>
> Where's the problem? pdb2gmx makes a .top file for your non-special
> system, you #include the .itp file for your special part. There's
> nothing about atomic positions yet have a look at a .top file. Now
> grompp takes the .top and some file with atomic positions and makes a
> .tpr file. Same general procedure as normal.
>
> Mark
> ___
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Re: [gmx-users] special molecule
I think you can use editconf to convert your original pdb to a gro file.
On Mon, 2006-06-12 at 13:48 +, Tamas Horvath wrote:
> As I understand, if there are "special" molecules in a pdb file,
> pdb2gmx cannot convert it. However, PRODRG can create an *.itp file
> for that molecule, so that I can include it in the generated topology
> file. But how can I place the molecule in it's original position? Or
> even better, how can I convert the original ("full") .pdb file for
> gromacs?
> ___
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Re: [gmx-users] special molecule
Tamas Horvath wrote:
As I understand, if there are "special" molecules in a pdb file, pdb2gmx
cannot convert it. However, PRODRG can create an *.itp file for that
molecule, so that I can include it in the generated topology file. But
how can I place the molecule in it's original position? Or even better,
how can I convert the original ("full") .pdb file for gromacs?
Where's the problem? pdb2gmx makes a .top file for your non-special
system, you #include the .itp file for your special part. There's
nothing about atomic positions yet have a look at a .top file. Now
grompp takes the .top and some file with atomic positions and makes a
.tpr file. Same general procedure as normal.
Mark
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