Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Daniele Veclani 
Dear Peter Stern.

Yes, I need the starting coordination for methanol, but are there specific
coordinates like for spce water or tip3p water?

Where can I find the files .gro or .pdb for methanol ?


Dear Chaban

Similar molecules have already been studied with this methanol.

This Methanol is implemented in opls force field.

I appreciate the time and effort you have spent sorting out that problem.

D.V.


2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:

> On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com> wrote:
>
> > You, perhaps, need to care about *compatibility* of this old methanol and
> > your solute molecule.
> >
>
>
> Why? General caution or do you know that there is something wrong with it?
> Because if I'm not mistaken, it's the same methanol distributed with
> Gromacs.
>
> All the best,
> Kalev
>
> >
> >
> >
> >
> >
> > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <peter.st...@weizmann.ac.il>
> > wrote:
> >
> > > The force field parameters are defined in ffbonded.itp and
> > ffnonbonded.itp.
> > > You still need starting coordinates for your molecule.
> > > There are plenty of programs which will do this, but you can probably
> > find
> > > it in some pdb entry.
> > > But, it is also trivial to do by hand since there are only two atoms
> and
> > > you know the C-O bond distance, e.g.:
> > > HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
> > > HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
> > >
> > > You should use an existing pdb or gro file as a template for the
> correct
> > > format.  gmx pdb2gmx will add the H-atoms.
> > >
> > > Peter Stern
> > >
> > > -Original Message-----
> > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> Daniele
> > > Veclani
> > > Sent: Thursday, December 03, 2015 3:31 PM
> > > To: gmx-us...@gromacs.org
> > > Subject: Re: [gmx-users] Methanol geometry parameters
> > >
> > > Thank you for your reply.
> > >
> > > Yes, The .itp file for methanol comes from gromacs. But but I need the
> > > .gro file. I need the geometric parameters like distances, angles and
> > > diedrals.
> > > these parameters are not in the .itp file or I'm wrong??
> > >
> > > Best regards
> > > D.V.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
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> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
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> > > posting!
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Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Barnett, James W 
On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
> Dear Peter Stern.
> 
> Yes, I need the starting coordination for methanol, but are there specific
> coordinates like for spce water or tip3p water?
> 
> Where can I find the files .gro or .pdb for methanol ?

Creating a methanol pdb file should be quick with a program like Avogadro or
maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for water.

> 
> 
> Dear Chaban
> 
> Similar molecules have already been studied with this methanol.
> 
> This Methanol is implemented in opls force field.
> 
> I appreciate the time and effort you have spent sorting out that problem.
> 
> D.V.
> 
> 
> 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:
> 
> > On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com> wrote:
> > 
> > > You, perhaps, need to care about *compatibility* of this old methanol and
> > > your solute molecule.
> > > 
> > 
> > 
> > Why? General caution or do you know that there is something wrong with it?
> > Because if I'm not mistaken, it's the same methanol distributed with
> > Gromacs.
> > 
> > All the best,
> > Kalev
> > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <peter.st...@weizmann.ac.il>
> > > wrote:
> > > 
> > > > The force field parameters are defined in ffbonded.itp and
> > > ffnonbonded.itp.
> > > > You still need starting coordinates for your molecule.
> > > > There are plenty of programs which will do this, but you can probably
> > > find
> > > > it in some pdb entry.
> > > > But, it is also trivial to do by hand since there are only two atoms
> > and
> > > > you know the C-O bond distance, e.g.:
> > > > HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
> > > > HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
> > > > 
> > > > You should use an existing pdb or gro file as a template for the
> > correct
> > > > format.  gmx pdb2gmx will add the H-atoms.
> > > > 
> > > > Peter Stern
> > > > 
> > > > -Original Message-
> > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> > Daniele
> > > > Veclani
> > > > Sent: Thursday, December 03, 2015 3:31 PM
> > > > To: gmx-us...@gromacs.org
> > > > Subject: Re: [gmx-users] Methanol geometry parameters
> > > > 
> > > > Thank you for your reply.
> > > > 
> > > > Yes, The .itp file for methanol comes from gromacs. But but I need the
> > > > .gro file. I need the geometric parameters like distances, angles and
> > > > diedrals.
> > > > these parameters are not in the .itp file or I'm wrong??
> > > > 
> > > > Best regards
> > > > D.V.
> > > > --
> > > > Gromacs Users mailing list
> > > > 
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > > 
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > 
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > --
> > > > Gromacs Users mailing list
> > > > 
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> > > > posting!
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> > > > 
> > > --
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Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Daniele Veclani 
Dear Stern.

 I apologize for the disruption.

Create pdb file is very simple. but the distances and bond angles of
methanol where I find them?

I do not think can I put random distances and angles?

Best
D.V.



2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>:

> On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
> > Dear Peter Stern.
> >
> > Yes, I need the starting coordination for methanol, but are there
> specific
> > coordinates like for spce water or tip3p water?
> >
> > Where can I find the files .gro or .pdb for methanol ?
>
> Creating a methanol pdb file should be quick with a program like Avogadro
> or
> maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for
> water.
>
> >
> >
> > Dear Chaban
> >
> > Similar molecules have already been studied with this methanol.
> >
> > This Methanol is implemented in opls force field.
> >
> > I appreciate the time and effort you have spent sorting out that problem.
> >
> > D.V.
> >
> >
> > 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:
> >
> > > On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com>
> wrote:
> > >
> > > > You, perhaps, need to care about *compatibility* of this old
> methanol and
> > > > your solute molecule.
> > > >
> > >
> > >
> > > Why? General caution or do you know that there is something wrong with
> it?
> > > Because if I'm not mistaken, it's the same methanol distributed with
> > > Gromacs.
> > >
> > > All the best,
> > > Kalev
> > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <
> peter.st...@weizmann.ac.il>
> > > > wrote:
> > > >
> > > > > The force field parameters are defined in ffbonded.itp and
> > > > ffnonbonded.itp.
> > > > > You still need starting coordinates for your molecule.
> > > > > There are plenty of programs which will do this, but you can
> probably
> > > > find
> > > > > it in some pdb entry.
> > > > > But, it is also trivial to do by hand since there are only two
> atoms
> > > and
> > > > > you know the C-O bond distance, e.g.:
> > > > > HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
> > > > > HETATM    2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
> > > > >
> > > > > You should use an existing pdb or gro file as a template for the
> > > correct
> > > > > format.  gmx pdb2gmx will add the H-atoms.
> > > > >
> > > > > Peter Stern
> > > > >
> > > > > -Original Message-
> > > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> > > > > gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
> > > Daniele
> > > > > Veclani
> > > > > Sent: Thursday, December 03, 2015 3:31 PM
> > > > > To: gmx-us...@gromacs.org
> > > > > Subject: Re: [gmx-users] Methanol geometry parameters
> > > > >
> > > > > Thank you for your reply.
> > > > >
> > > > > Yes, The .itp file for methanol comes from gromacs. But but I need
> the
> > > > > .gro file. I need the geometric parameters like distances, angles
> and
> > > > > diedrals.
> > > > > these parameters are not in the .itp file or I'm wrong??
> > > > >
> > > > > Best regards
> > > > > D.V.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > > posting!
> > > > >
> > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > > >
> > > > > * For (un)subscribe requests visit
> > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > > send a mail to gmx-users-requ...@gromacs.org.
> > > > > --
> > > > > Gromacs Users mailing list
> > > > >
> > > > > * Please search the archive at
> > > > > http://www.gromacs.org/Support/Mailing_L

Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Peter Stern 
And there are no bond angles in methanol aside from the ones involving hydrogen 
atoms and these are added automatically by pdb2gmx.
As I already wrote, and Justin pointed out, the only geometric information that 
you need is the C-O bond length, which is given in the force field Ito file.  
For water there are no coordinates, just the single O atom.  Again, H's are 
added.

Sent from my iPhone

> On 4 Dec 2015, at 2:39 PM, Daniele Veclani <danielevecl...@gmail.com> wrote:
> 
> Dear Stern.
> 
> I apologize for the disruption.
> 
> Create pdb file is very simple. but the distances and bond angles of
> methanol where I find them?
> 
> I do not think can I put random distances and angles?
> 
> Best
> D.V.
> 
> 
> 
> 2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>:
> 
>>> On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
>>> Dear Peter Stern.
>>> 
>>> Yes, I need the starting coordination for methanol, but are there
>> specific
>>> coordinates like for spce water or tip3p water?
>>> 
>>> Where can I find the files .gro or .pdb for methanol ?
>> 
>> Creating a methanol pdb file should be quick with a program like Avogadro
>> or
>> maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for
>> water.
>> 
>>> 
>>> 
>>> Dear Chaban
>>> 
>>> Similar molecules have already been studied with this methanol.
>>> 
>>> This Methanol is implemented in opls force field.
>>> 
>>> I appreciate the time and effort you have spent sorting out that problem.
>>> 
>>> D.V.
>>> 
>>> 
>>> 2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:
>>> 
>>>> On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com>
>> wrote:
>>>> 
>>>>> You, perhaps, need to care about *compatibility* of this old
>> methanol and
>>>>> your solute molecule.
>>>> 
>>>> 
>>>> Why? General caution or do you know that there is something wrong with
>> it?
>>>> Because if I'm not mistaken, it's the same methanol distributed with
>>>> Gromacs.
>>>> 
>>>> All the best,
>>>> Kalev
>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <
>> peter.st...@weizmann.ac.il>
>>>>> wrote:
>>>>> 
>>>>>> The force field parameters are defined in ffbonded.itp and
>>>>> ffnonbonded.itp.
>>>>>> You still need starting coordinates for your molecule.
>>>>>> There are plenty of programs which will do this, but you can
>> probably
>>>>> find
>>>>>> it in some pdb entry.
>>>>>> But, it is also trivial to do by hand since there are only two
>> atoms
>>>> and
>>>>>> you know the C-O bond distance, e.g.:
>>>>>> HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
>>>>>> HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
>>>>>> 
>>>>>> You should use an existing pdb or gro file as a template for the
>>>> correct
>>>>>> format.  gmx pdb2gmx will add the H-atoms.
>>>>>> 
>>>>>> Peter Stern
>>>>>> 
>>>>>> -Original Message-
>>>>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
>>>>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of
>>>> Daniele
>>>>>> Veclani
>>>>>> Sent: Thursday, December 03, 2015 3:31 PM
>>>>>> To: gmx-us...@gromacs.org
>>>>>> Subject: Re: [gmx-users] Methanol geometry parameters
>>>>>> 
>>>>>> Thank you for your reply.
>>>>>> 
>>>>>> Yes, The .itp file for methanol comes from gromacs. But but I need
>> the
>>>>>> .gro file. I need the geometric parameters like distances, angles
>> and
>>>>>> diedrals.
>>>>>> these parameters are not in the .itp file or I'm wrong??
>>>>>> 
>>>>>> Best regards
>>>>>> D.V.
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>> 
>>>>>> * Please sea

Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Justin Lemkul 



On 12/4/15 8:01 AM, Peter Stern wrote:

And there are no bond angles in methanol aside from the ones involving hydrogen 
atoms and these are added automatically by pdb2gmx.
As I already wrote, and Justin pointed out, the only geometric information that 
you need is the C-O bond length, which is given in the force field Ito file.  
For water there are no coordinates, just the single O atom.  Again, H's are 
added.



A quick note, though: H are only added if suitable entries are found in the 
force field .hdb file.  pdb2gmx does a lot of tricks, but it's not necessarily 
magic.


-Justin


Sent from my iPhone


On 4 Dec 2015, at 2:39 PM, Daniele Veclani <danielevecl...@gmail.com> wrote:

Dear Stern.

I apologize for the disruption.

Create pdb file is very simple. but the distances and bond angles of
methanol where I find them?

I do not think can I put random distances and angles?

Best
D.V.



2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>:


On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:
Dear Peter Stern.

Yes, I need the starting coordination for methanol, but are there

specific

coordinates like for spce water or tip3p water?

Where can I find the files .gro or .pdb for methanol ?


Creating a methanol pdb file should be quick with a program like Avogadro
or
maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for
water.




Dear Chaban

Similar molecules have already been studied with this methanol.

This Methanol is implemented in opls force field.

I appreciate the time and effort you have spent sorting out that problem.

D.V.


2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:


On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com>

wrote:



You, perhaps, need to care about *compatibility* of this old

methanol and

your solute molecule.



Why? General caution or do you know that there is something wrong with

it?

Because if I'm not mistaken, it's the same methanol distributed with
Gromacs.

All the best,
Kalev







On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <

peter.st...@weizmann.ac.il>

wrote:


The force field parameters are defined in ffbonded.itp and

ffnonbonded.itp.

You still need starting coordinates for your molecule.
There are plenty of programs which will do this, but you can

probably

find

it in some pdb entry.
But, it is also trivial to do by hand since there are only two

atoms

and

you know the C-O bond distance, e.g.:
HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00

You should use an existing pdb or gro file as a template for the

correct

format.  gmx pdb2gmx will add the H-atoms.

Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of

Daniele

Veclani
Sent: Thursday, December 03, 2015 3:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Methanol geometry parameters

Thank you for your reply.

Yes, The .itp file for methanol comes from gromacs. But but I need

the

.gro file. I need the geometric parameters like distances, angles

and

diedrals.
these parameters are not in the .itp file or I'm wrong??

Best regards
D.V.
--
Gromacs Users mailing list

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--
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisia

Re: [gmx-users] Methanol geometry parameters

2015-12-04 Thread Justin Lemkul 



On 12/4/15 7:38 AM, Daniele Veclani wrote:

Dear Stern.

  I apologize for the disruption.

Create pdb file is very simple. but the distances and bond angles of
methanol where I find them?

I do not think can I put random distances and angles?



Why do you need this information?  All bonded parameters are in ffbonded.itp, so 
you can reference those values.  Just look up the interaction by the atom types 
involved.


-Justin


Best
D.V.



2015-12-04 12:50 GMT+01:00 Barnett, James W <jbarn...@tulane.edu>:


On Fri, 2015-12-04 at 09:43 +0100, Daniele Veclani wrote:

Dear Peter Stern.

Yes, I need the starting coordination for methanol, but are there

specific

coordinates like for spce water or tip3p water?

Where can I find the files .gro or .pdb for methanol ?


Creating a methanol pdb file should be quick with a program like Avogadro
or
maybe AmberTool's xleap. Then use "gmx solvate" to get coordinates for
water.




Dear Chaban

Similar molecules have already been studied with this methanol.

This Methanol is implemented in opls force field.

I appreciate the time and effort you have spent sorting out that problem.

D.V.


2015-12-04 8:41 GMT+01:00 Kalev Takkis <kalev.tak...@gmail.com>:


On 3 December 2015 at 20:05, Vitaly V. Chaban <vvcha...@gmail.com>

wrote:



You, perhaps, need to care about *compatibility* of this old

methanol and

your solute molecule.




Why? General caution or do you know that there is something wrong with

it?

Because if I'm not mistaken, it's the same methanol distributed with
Gromacs.

All the best,
Kalev







On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <

peter.st...@weizmann.ac.il>

wrote:


The force field parameters are defined in ffbonded.itp and

ffnonbonded.itp.

You still need starting coordinates for your molecule.
There are plenty of programs which will do this, but you can

probably

find

it in some pdb entry.
But, it is also trivial to do by hand since there are only two

atoms

and

you know the C-O bond distance, e.g.:
HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00

You should use an existing pdb or gro file as a template for the

correct

format.  gmx pdb2gmx will add the H-atoms.

Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of

Daniele

Veclani
Sent: Thursday, December 03, 2015 3:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Methanol geometry parameters

Thank you for your reply.

Yes, The .itp file for methanol comes from gromacs. But but I need

the

.gro file. I need the geometric parameters like distances, angles

and

diedrals.
these parameters are not in the .itp file or I'm wrong??

Best regards
D.V.
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--
James "Wes" Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarn...@tulane.edu
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--
==

Justin A. Lemkul,

Re: [gmx-users] Methanol geometry parameters

2015-12-03 Thread chandan patel 
Hi,
I believe oplsaa itp for methanol comes with gromacs5.1. Alternatively you
can download parameters from virtual chemistry.org

Best,
CP
On Dec 3, 2015 3:02 PM, "Daniele Veclani"  wrote:

> Dear all.
>
> I want to study a molecule using methanol as solvent.
>
> I have some problem to understanding which geometry of methanol is used by
> the OPLS- all atom force field (JACS, 1996, 118, 11225). In the paper
> published on JACS in 1996 there are no details on the geometries of the
> models they are parametrizing.
> Moreover, do you know if I can find somewhere the topology file for this
> methanol model (from the download topologies page I've downloaded the
> topology but there are no geometric parameters like distances, angles and
> diedrals.)
>
> Thank you in advance
>
> D.V.
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Re: [gmx-users] Methanol geometry parameters

2015-12-03 Thread Daniele Veclani 
Thank you for your reply.

Yes, The .itp file for methanol comes from gromacs. But but I need the .gro
file. I need the geometric parameters like distances, angles and diedrals.
these parameters are not in the .itp file or I'm wrong??

Best regards
D.V.
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Re: [gmx-users] Methanol geometry parameters

2015-12-03 Thread Peter Stern 
The force field parameters are defined in ffbonded.itp and ffnonbonded.itp.
You still need starting coordinates for your molecule.
There are plenty of programs which will do this, but you can probably find it 
in some pdb entry.
But, it is also trivial to do by hand since there are only two atoms and you 
know the C-O bond distance, e.g.:
HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00  
HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00   

You should use an existing pdb or gro file as a template for the correct 
format.  gmx pdb2gmx will add the H-atoms.

Peter Stern

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Daniele 
Veclani
Sent: Thursday, December 03, 2015 3:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Methanol geometry parameters

Thank you for your reply.

Yes, The .itp file for methanol comes from gromacs. But but I need the .gro 
file. I need the geometric parameters like distances, angles and diedrals.
these parameters are not in the .itp file or I'm wrong??

Best regards
D.V.
--
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Re: [gmx-users] Methanol geometry parameters

2015-12-03 Thread Vitaly V. Chaban 
You, perhaps, need to care about *compatibility* of this old methanol and
your solute molecule.





On Thu, Dec 3, 2015 at 2:08 PM, Peter Stern <peter.st...@weizmann.ac.il>
wrote:

> The force field parameters are defined in ffbonded.itp and ffnonbonded.itp.
> You still need starting coordinates for your molecule.
> There are plenty of programs which will do this, but you can probably find
> it in some pdb entry.
> But, it is also trivial to do by hand since there are only two atoms and
> you know the C-O bond distance, e.g.:
> HETATM1  C   MOH  1  1   0.000   0.000   1.410  1.00  1.00
> HETATM2  O  MOH  1  1   0.000   0.000   0.000  1.00  1.00
>
> You should use an existing pdb or gro file as a template for the correct
> format.  gmx pdb2gmx will add the H-atoms.
>
> Peter Stern
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Daniele
> Veclani
> Sent: Thursday, December 03, 2015 3:31 PM
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Methanol geometry parameters
>
> Thank you for your reply.
>
> Yes, The .itp file for methanol comes from gromacs. But but I need the
> .gro file. I need the geometric parameters like distances, angles and
> diedrals.
> these parameters are not in the .itp file or I'm wrong??
>
> Best regards
> D.V.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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