Re: [gmx-users] gromos parameterisation in OPLS

2008-06-17 Thread Justin A. Lemkul 
If you include in the .itp file all the necessary combinations in those 
sections, then yes, the .itp file is reasonable and will use the OPLS-AA 
parameters for those specified items.  Take care to get the numbering 
right after that point, because you will likely be inserting lots of 
hydrogens!


-Justin

ANINDITA GAYEN wrote:

Sir,

If i insert the hydrogen atoms in the first section of the itp file, where atomnames , 
atomtypes , nr, cgnr are displayed, wil it be wrong. Also, i was talking that, will the 
inclusion of "ffoplsaa.itp" will serve the bonded and nonbonded parameters if i 
supply the connectivities in all the bonds, pairs, angles and dihedral section by the 
atom numbers?

Thanks for the requested answers.

anindita




--- On Mon, 16/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

  

From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation in OPLS
To: [EMAIL PROTECTED], "Discussion list for GROMACS users" 

Date: Monday, 16 June, 2008, 9:29 PM
Changing the atomtypes will only work if you have explicit
inclusion of 
all hydrogens in your PRODRG-generated topology.  Since the
PRODRG 
server outputs a GROMOS-based .itp file, this is unlikely
unless your 
molecule contains only polar or aromatic groups.  If
we're still talking 
about CHAPS or cholesterol, this will not be the case.  You
will have 
nonpolar groups that, within GROMOS, are atomtype CH1, CH2,
etc., but 
OPLS will not have these UA representations.


I'm not sure what you mean in the last sentence. 
Nothing in this 
process will be automatically generated for you. 
You're building your 
topology by hand.  Inclusion of "ffoplsaa.itp"
will tell grompp which 
parameters (bonded and nonbonded) apply to your molecule. 
Calling 
"ffoplsaa.itp" will not tell any Gromacs program
to automatically detect 
and generate bonds, dihedrals, etc. 


The only way to have "automatic" generation of
these parameters is to 
build an .rtp entry for your molecule that contains all of
this 
information as well, and process your structure with
pdb2gmx.  This is 
just as much work as building the topology yourself, I

think.

-Justin

ANINDITA GAYEN wrote:


Hi,

I came to know from the mailing list that if i only
  

change the atomtype in the output itp file of PRODRG2 and
put the charges as optimised by Gaussian; provided i
include #include ffoplsaa.itp in the .top file of the new
molecule and just keep the atom mumbers in [bonds],
[pairs], [angles] and [dihedrals] as found in the the all
atom pdb of PRODRG2, the resultant top file will be a top
file in OPLS format. It was also stated there in the
mailing list that for the atom numbers mentioned the opls
staff will put the parameter values necccesary for the
[bonds], [angles] etc.

Is the approach right? 







  From Chandigarh to Chennai - find friends all
  

over India. Go to
http://in.promos.yahoo.com/groups/citygroups/


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Virginia Tech
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin



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Re: [gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

2008-06-17 Thread Florian Dommert 
Vitaly Chaban wrote:

>> I've got a discrepancy calculating the diffusion coefficient via
>> Green-Kubo equation and via Einstein equation.
>> 
>
>   
>> $ g_velacc -nonormalize -acflen 1001
>> $ g_analyze -f vac.xvg -integrate
>> Do I miss any important keyword here? It seems the result of integration is 
>> not
>> correct in this case.
>> 
>
> For the VACF of the molecules:
> $ g_velacc -nonormalize -acflen 1001 -mol -n index.ndx (index.ndx
> contains the number of molecules for the calculation)
>
> $ g_analyze -f vac.xvg -integrate
>
> The result should be finally divided by 3.
>
>   
Hello,

 why should one use a prefactor of 1.0/3.0 ? I thought the flag -mol
calculates
the momentum autocorrelation function, so in my opinion the result has
to be divided
by the square of the masses of the molecules to obtain the diffusion
constant.

Best Regards,

 Flo


> --
> Vitaly V. Chaban
> School of Chemistry
> University of Kharkiv
> Svobody sq.,4
> Kharkiv 61077, Ukraine
>
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to [EMAIL PROTECTED]
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>
>   


-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: [EMAIL PROTECTED]
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert




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[gmx-users] regarding trjconv

2008-06-17 Thread Anamika Awasthi 
Dear all,
RMSD and RMSF of my protein is showing abnormal flucutuation. To
overcome this problem I am using following commands-->
  trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole

  trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump

   but this second command is showing fatal error:
  Index[35] 334 is larger than the number of atoms in the
trajectory file (330)
 pls help me to understand this and to sort out this problem.

   Thank you
 Anamika
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Re: [gmx-users] gromos parameterisation in OPLS

2008-06-17 Thread ANINDITA GAYEN 


can i put the partial charges from Gaussian?
--- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> Subject: Re: [gmx-users] gromos parameterisation in OPLS
> To: [EMAIL PROTECTED], "Gromacs Users' List" 
> Date: Tuesday, 17 June, 2008, 4:00 PM
> If you include in the .itp file all the necessary
> combinations in those 
> sections, then yes, the .itp file is reasonable and will
> use the OPLS-AA 
> parameters for those specified items.  Take care to get the
> numbering 
> right after that point, because you will likely be
> inserting lots of 
> hydrogens!
> 
> -Justin
> 
> ANINDITA GAYEN wrote:
> > Sir,
> >
> > If i insert the hydrogen atoms in the first section of
> the itp file, where atomnames , atomtypes , nr, cgnr are
> displayed, wil it be wrong. Also, i was talking that, will
> the inclusion of "ffoplsaa.itp" will serve the
> bonded and nonbonded parameters if i supply the
> connectivities in all the bonds, pairs, angles and dihedral
> section by the atom numbers?
> >
> > Thanks for the requested answers.
> >
> > anindita
> >
> >
> >
> >
> > --- On Mon, 16/6/08, Justin A. Lemkul
> <[EMAIL PROTECTED]> wrote:
> >
> >   
> >> From: Justin A. Lemkul <[EMAIL PROTECTED]>
> >> Subject: Re: [gmx-users] gromos parameterisation
> in OPLS
> >> To: [EMAIL PROTECTED], "Discussion
> list for GROMACS users" 
> >> Date: Monday, 16 June, 2008, 9:29 PM
> >> Changing the atomtypes will only work if you have
> explicit
> >> inclusion of 
> >> all hydrogens in your PRODRG-generated topology. 
> Since the
> >> PRODRG 
> >> server outputs a GROMOS-based .itp file, this is
> unlikely
> >> unless your 
> >> molecule contains only polar or aromatic groups. 
> If
> >> we're still talking 
> >> about CHAPS or cholesterol, this will not be the
> case.  You
> >> will have 
> >> nonpolar groups that, within GROMOS, are atomtype
> CH1, CH2,
> >> etc., but 
> >> OPLS will not have these UA representations.
> >>
> >> I'm not sure what you mean in the last
> sentence. 
> >> Nothing in this 
> >> process will be automatically generated for you. 
> >> You're building your 
> >> topology by hand.  Inclusion of
> "ffoplsaa.itp"
> >> will tell grompp which 
> >> parameters (bonded and nonbonded) apply to your
> molecule. 
> >> Calling 
> >> "ffoplsaa.itp" will not tell any Gromacs
> program
> >> to automatically detect 
> >> and generate bonds, dihedrals, etc. 
> >>
> >> The only way to have "automatic"
> generation of
> >> these parameters is to 
> >> build an .rtp entry for your molecule that
> contains all of
> >> this 
> >> information as well, and process your structure
> with
> >> pdb2gmx.  This is 
> >> just as much work as building the topology
> yourself, I
> >> think.
> >>
> >> -Justin
> >>
> >> ANINDITA GAYEN wrote:
> >> 
> >>> Hi,
> >>>
> >>> I came to know from the mailing list that if i
> only
> >>>   
> >> change the atomtype in the output itp file of
> PRODRG2 and
> >> put the charges as optimised by Gaussian; provided
> i
> >> include #include ffoplsaa.itp in the .top file of
> the new
> >> molecule and just keep the atom mumbers in
> [bonds],
> >> [pairs], [angles] and [dihedrals] as found in the
> the all
> >> atom pdb of PRODRG2, the resultant top file will
> be a top
> >> file in OPLS format. It was also stated there in
> the
> >> mailing list that for the atom numbers mentioned
> the opls
> >> staff will put the parameter values necccesary for
> the
> >> [bonds], [angles] etc.
> >> 
> >>> Is the approach right? 
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>   From Chandigarh to Chennai - find
> friends all
> >>>   
> >> over India. Go to
> >> http://in.promos.yahoo.com/groups/citygroups/
> >> 
> >>>
> ___
> >>> gmx-users mailing list   
> gmx-users@gromacs.org
> >>>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> >>> Please search the archive at
> >>>   
> >> http://www.gromacs.org/search before posting!
> >> 
> >>> 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
> >> 
> >>>   
> >>>   
> >> -- 
> >> 
> >>
> >> Justin A. Lemkul
> >> Graduate Research Assistant
> >> Department of Biochemistry
> >> Virginia Tech
> >> Blacksburg, VA
> >> jalemkul[at]vt.edu | (540) 231-9080
> >>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >>
> >> 
> >> 
> >
> >
> >   Connect with friends all over the world. Get
> Yahoo! India Messenger at
> http://in.messenger.yahoo.com/?wm=n/
> >
> >
> >   
> 
> -- 
> 
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)

Re: [gmx-users] gromos parameterisation in OPLS

2008-06-17 Thread Justin A. Lemkul 
Parameterization should always be done according to the derivation of 
the original force field.  I don't know all the specifics of the OPLS-AA 
parameterization, so you'll have to look into it. 


-Justin

ANINDITA GAYEN wrote:

can i put the partial charges from Gaussian?
--- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

  

From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation in OPLS
To: [EMAIL PROTECTED], "Gromacs Users' List" 
Date: Tuesday, 17 June, 2008, 4:00 PM
If you include in the .itp file all the necessary
combinations in those 
sections, then yes, the .itp file is reasonable and will
use the OPLS-AA 
parameters for those specified items.  Take care to get the
numbering 
right after that point, because you will likely be
inserting lots of 
hydrogens!


-Justin

ANINDITA GAYEN wrote:


Sir,

If i insert the hydrogen atoms in the first section of
  

the itp file, where atomnames , atomtypes , nr, cgnr are
displayed, wil it be wrong. Also, i was talking that, will
the inclusion of "ffoplsaa.itp" will serve the
bonded and nonbonded parameters if i supply the
connectivities in all the bonds, pairs, angles and dihedral
section by the atom numbers?


Thanks for the requested answers.

anindita




--- On Mon, 16/6/08, Justin A. Lemkul
  

<[EMAIL PROTECTED]> wrote:

  
  

From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation


in OPLS


To: [EMAIL PROTECTED], "Discussion


list for GROMACS users" 


Date: Monday, 16 June, 2008, 9:29 PM
Changing the atomtypes will only work if you have


explicit

inclusion of 
all hydrogens in your PRODRG-generated topology. 


Since the

PRODRG 
server outputs a GROMOS-based .itp file, this is


unlikely

unless your 
molecule contains only polar or aromatic groups. 


If

we're still talking 
about CHAPS or cholesterol, this will not be the


case.  You

will have 
nonpolar groups that, within GROMOS, are atomtype


CH1, CH2,

etc., but 
OPLS will not have these UA representations.


I'm not sure what you mean in the last

sentence. 

Nothing in this 
process will be automatically generated for you. 
You're building your 
topology by hand.  Inclusion of


"ffoplsaa.itp"

will tell grompp which 
parameters (bonded and nonbonded) apply to your

molecule. 

Calling 
"ffoplsaa.itp" will not tell any Gromacs


program

to automatically detect 
and generate bonds, dihedrals, etc. 


The only way to have "automatic"


generation of

these parameters is to 
build an .rtp entry for your molecule that


contains all of

this 
information as well, and process your structure


with

pdb2gmx.  This is 
just as much work as building the topology


yourself, I


think.

-Justin

ANINDITA GAYEN wrote:



Hi,

I came to know from the mailing list that if i
  

only

  
  

change the atomtype in the output itp file of


PRODRG2 and


put the charges as optimised by Gaussian; provided


i


include #include ffoplsaa.itp in the .top file of


the new


molecule and just keep the atom mumbers in


[bonds],


[pairs], [angles] and [dihedrals] as found in the


the all


atom pdb of PRODRG2, the resultant top file will


be a top


file in OPLS format. It was also stated there in


the


mailing list that for the atom numbers mentioned


the opls


staff will put the parameter values necccesary for


the


[bonds], [angles] etc.


Is the approach right? 







  From Chandigarh to Chennai - find
  

friends all

  
  

over India. Go to
http://in.promos.yahoo.com/groups/citygroups/



___

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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080



http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin






  Connect with friends all over the world. Get
  

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Re: [gmx-users] Re[4]: g_msd vs g_velacc. [SOLVED]

2008-06-17 Thread Florian Dommert 
Florian Dommert wrote:

> Vitaly Chaban wrote:
>
>   
>>> I've got a discrepancy calculating the diffusion coefficient via
>>> Green-Kubo equation and via Einstein equation.
>>> 
>>>   
>>   
>> 
>>> $ g_velacc -nonormalize -acflen 1001
>>> $ g_analyze -f vac.xvg -integrate
>>> Do I miss any important keyword here? It seems the result of integration is 
>>> not
>>> correct in this case.
>>> 
>>>   
>> For the VACF of the molecules:
>> $ g_velacc -nonormalize -acflen 1001 -mol -n index.ndx (index.ndx
>> contains the number of molecules for the calculation)
>>
>> $ g_analyze -f vac.xvg -integrate
>>
>> The result should be finally divided by 3.
>>
>>   
>> 
> Hello,
>
>  why should one use a prefactor of 1.0/3.0 ? 
Hi,

 after inspecting a suitable paper (
http://prola.aps.org/abstract/PRA/v11/i6/p2111_1), I got
the prefactor. Sorry for the confusion.

Best Regards

Flo



> I thought the flag -mol
> calculates
> the momentum autocorrelation function, so in my opinion the result has
> to be divided
> by the square of the masses of the molecules to obtain the diffusion
> constant.
>
> Best Regards,
>
>  Flo
>
>
>   
>> --
>> Vitaly V. Chaban
>> School of Chemistry
>> University of Kharkiv
>> Svobody sq.,4
>> Kharkiv 61077, Ukraine
>>
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> 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
>>
>>   
>> 
>
>
>   
> 
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> 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


-- 
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: [EMAIL PROTECTED]
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert




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Re: [gmx-users] gromos parameterisation in OPLS

2008-06-17 Thread Xavier Periole 

On Tue, 17 Jun 2008 17:31:53 +0530 (IST)
 ANINDITA GAYEN <[EMAIL PROTECTED]> wrote:



can i put the partial charges from Gaussian?

In principle you can do everything assuming that it is justified.

Putting charges from Gaussian do not mean much. It sounds very elaborated
because Gaussian could imply that you include "ab initio" calculations.
However Gaussian also include semi-empirical methods!

All that to say that the manner the charges are extracted from Gaussian
is much more relevant to be able to judge their quality.

What you have to do is to convince yourself that the way you do is the
accurate enough to the application you like.

In a general manner the RESP (see Amber web site) approach has shown
to be relative reliable.


--- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:


From: Justin A. Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] gromos parameterisation in OPLS
To: [EMAIL PROTECTED], "Gromacs Users' List" 
Date: Tuesday, 17 June, 2008, 4:00 PM
If you include in the .itp file all the necessary
combinations in those 
sections, then yes, the .itp file is reasonable and will
use the OPLS-AA 
parameters for those specified items.  Take care to get the
numbering 
right after that point, because you will likely be
inserting lots of 
hydrogens!


-Justin

ANINDITA GAYEN wrote:
> Sir,
>
> If i insert the hydrogen atoms in the first section of
the itp file, where atomnames , atomtypes , nr, cgnr are
displayed, wil it be wrong. Also, i was talking that, will
the inclusion of "ffoplsaa.itp" will serve the
bonded and nonbonded parameters if i supply the
connectivities in all the bonds, pairs, angles and dihedral
section by the atom numbers?
>
> Thanks for the requested answers.
>
> anindita
>
>
>
>
> --- On Mon, 16/6/08, Justin A. Lemkul
<[EMAIL PROTECTED]> wrote:
>
>   
>> From: Justin A. Lemkul <[EMAIL PROTECTED]>

>> Subject: Re: [gmx-users] gromos parameterisation
in OPLS
>> To: [EMAIL PROTECTED], "Discussion
list for GROMACS users" 
>> Date: Monday, 16 June, 2008, 9:29 PM
>> Changing the atomtypes will only work if you have
explicit
>> inclusion of 
>> all hydrogens in your PRODRG-generated topology. 
Since the
>> PRODRG 
>> server outputs a GROMOS-based .itp file, this is

unlikely
>> unless your 
>> molecule contains only polar or aromatic groups. 
If
>> we're still talking 
>> about CHAPS or cholesterol, this will not be the

case.  You
>> will have 
>> nonpolar groups that, within GROMOS, are atomtype

CH1, CH2,
>> etc., but 
>> OPLS will not have these UA representations.

>>
>> I'm not sure what you mean in the last
sentence. 
>> Nothing in this 
>> process will be automatically generated for you. 
>> You're building your 
>> topology by hand.  Inclusion of

"ffoplsaa.itp"
>> will tell grompp which 
>> parameters (bonded and nonbonded) apply to your
molecule. 
>> Calling 
>> "ffoplsaa.itp" will not tell any Gromacs

program
>> to automatically detect 
>> and generate bonds, dihedrals, etc. 
>>

>> The only way to have "automatic"
generation of
>> these parameters is to 
>> build an .rtp entry for your molecule that

contains all of
>> this 
>> information as well, and process your structure

with
>> pdb2gmx.  This is 
>> just as much work as building the topology

yourself, I
>> think.
>>
>> -Justin
>>
>> ANINDITA GAYEN wrote:
>> 
>>> Hi,

>>>
>>> I came to know from the mailing list that if i
only
>>>   
>> change the atomtype in the output itp file of

PRODRG2 and
>> put the charges as optimised by Gaussian; provided
i
>> include #include ffoplsaa.itp in the .top file of
the new
>> molecule and just keep the atom mumbers in
[bonds],
>> [pairs], [angles] and [dihedrals] as found in the
the all
>> atom pdb of PRODRG2, the resultant top file will
be a top
>> file in OPLS format. It was also stated there in
the
>> mailing list that for the atom numbers mentioned
the opls
>> staff will put the parameter values necccesary for
the
>> [bonds], [angles] etc.
>> 
>>> Is the approach right? 
>>>

>>>
>>>
>>>
>>>
>>>
>>>   From Chandigarh to Chennai - find
friends all
>>>   
>> over India. Go to

>> http://in.promos.yahoo.com/groups/citygroups/
>> 
>>>

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>>>
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>>> Please search the archive at
>>>   
>> http://www.gromacs.org/search before posting!
>> 
>>> 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
>> 
>>>   
>>>   
>> -- 
>> 

>>
>> Justin A. Lemkul
>> Graduate Research Assistant
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>>
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> =

[gmx-users] Re[5]: g_msd vs g_velacc. [SOLVED]

2008-06-17 Thread Vitaly Chaban 
> I thought the flag -mol
> calculates
> the momentum autocorrelation function, so in my opinion the result has
> to be divided
> by the square of the masses of the molecules to obtain the diffusion
> constant.

Flo, you're completely right. Sorry for my mistake as for
normalization here.

-- 
Vitaly

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Re: [gmx-users] gromos parameterisation in OPLS

2008-06-17 Thread Marc F. Lensink 
On Tue, Jun 17, 2008 at 02:21:09PM +0200, Xavier Periole wrote:
> On Tue, 17 Jun 2008 17:31:53 +0530 (IST)
>  ANINDITA GAYEN <[EMAIL PROTECTED]> wrote:
> >
> >
> >can i put the partial charges from Gaussian?
> In principle you can do everything assuming that it is justified.
> 
> Putting charges from Gaussian do not mean much. It sounds very elaborated
> because Gaussian could imply that you include "ab initio" calculations.
> However Gaussian also include semi-empirical methods!
> 
> All that to say that the manner the charges are extracted from Gaussian
> is much more relevant to be able to judge their quality.

although i would probably go for a b3lyp approach or so,
semi-empirally-derived charges are not necessarily a bad thing,
especially when a solvent reaction field was used.  in any case
they're a million times better than mulliken.

> What you have to do is to convince yourself that the way you do is the
> accurate enough to the application you like.
> 
> In a general manner the RESP (see Amber web site) approach has shown
> to be relative reliable.

agreed.

cheers,
marc


> >--- On Tue, 17/6/08, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> >
> >>From: Justin A. Lemkul <[EMAIL PROTECTED]>
> >>Subject: Re: [gmx-users] gromos parameterisation in OPLS
> >>To: [EMAIL PROTECTED], "Gromacs Users' List" 
> >>
> >>Date: Tuesday, 17 June, 2008, 4:00 PM
> >>If you include in the .itp file all the necessary
> >>combinations in those 
> >>sections, then yes, the .itp file is reasonable and will
> >>use the OPLS-AA 
> >>parameters for those specified items.  Take care to get the
> >>numbering 
> >>right after that point, because you will likely be
> >>inserting lots of 
> >>hydrogens!
> >>
> >>-Justin
> >>
> >>ANINDITA GAYEN wrote:
> >>> Sir,
> >>>
> >>> If i insert the hydrogen atoms in the first section of
> >>the itp file, where atomnames , atomtypes , nr, cgnr are
> >>displayed, wil it be wrong. Also, i was talking that, will
> >>the inclusion of "ffoplsaa.itp" will serve the
> >>bonded and nonbonded parameters if i supply the
> >>connectivities in all the bonds, pairs, angles and dihedral
> >>section by the atom numbers?
> >>>
> >>> Thanks for the requested answers.
> >>>
> >>> anindita
> >>>
> >>>
> >>>
> >>>
> >>> --- On Mon, 16/6/08, Justin A. Lemkul
> >><[EMAIL PROTECTED]> wrote:
> >>>
> >>>   
>  From: Justin A. Lemkul <[EMAIL PROTECTED]>
>  Subject: Re: [gmx-users] gromos parameterisation
> >>in OPLS
>  To: [EMAIL PROTECTED], "Discussion
> >>list for GROMACS users" 
>  Date: Monday, 16 June, 2008, 9:29 PM
>  Changing the atomtypes will only work if you have
> >>explicit
>  inclusion of 
>  all hydrogens in your PRODRG-generated topology. 
> >>Since the
>  PRODRG 
>  server outputs a GROMOS-based .itp file, this is
> >>unlikely
>  unless your 
>  molecule contains only polar or aromatic groups. 
> >>If
>  we're still talking 
>  about CHAPS or cholesterol, this will not be the
> >>case.  You
>  will have 
>  nonpolar groups that, within GROMOS, are atomtype
> >>CH1, CH2,
>  etc., but 
>  OPLS will not have these UA representations.
> 
>  I'm not sure what you mean in the last
> >>sentence. 
>  Nothing in this 
>  process will be automatically generated for you. 
>  You're building your 
>  topology by hand.  Inclusion of
> >>"ffoplsaa.itp"
>  will tell grompp which 
>  parameters (bonded and nonbonded) apply to your
> >>molecule. 
>  Calling 
>  "ffoplsaa.itp" will not tell any Gromacs
> >>program
>  to automatically detect 
>  and generate bonds, dihedrals, etc. 
> 
>  The only way to have "automatic"
> >>generation of
>  these parameters is to 
>  build an .rtp entry for your molecule that
> >>contains all of
>  this 
>  information as well, and process your structure
> >>with
>  pdb2gmx.  This is 
>  just as much work as building the topology
> >>yourself, I
>  think.
> 
>  -Justin
> 
>  ANINDITA GAYEN wrote:
>  
> > Hi,
> >
> > I came to know from the mailing list that if i
> >>only
> >   
>  change the atomtype in the output itp file of
> >>PRODRG2 and
>  put the charges as optimised by Gaussian; provided
> >>i
>  include #include ffoplsaa.itp in the .top file of
> >>the new
>  molecule and just keep the atom mumbers in
> >>[bonds],
>  [pairs], [angles] and [dihedrals] as found in the
> >>the all
>  atom pdb of PRODRG2, the resultant top file will
> >>be a top
>  file in OPLS format. It was also stated there in
> >>the
>  mailing list that for the atom numbers mentioned
> >>the opls
>  staff will put the parameter values necccesary for
> >>the
>  [bonds], [angles] etc.
>  
> > Is the approach right? 
> >
> >
> >
> >
> >
> >
> >   From Chandigarh to Chennai - find
> >>friends all
> >   
>  over India. Go to

Re: [gmx-users] regarding trjconv

2008-06-17 Thread Mark Abraham 

Anamika Awasthi wrote:

Dear all,
RMSD and RMSF of my protein is showing abnormal 
flucutuation. To overcome this problem I am using following commands-->

  trjconv -f *.trr -o trajout_whole.xtc -s *.tpr -pbc whole
   
  trjconv -f trajout_whole.xtc -o trajout_nojump .xtc -pbc nojump


   but this second command is showing fatal error:
  Index[35] 334 is larger than the number of atoms in the 
trajectory file (330)

 pls help me to understand this and to sort out this problem.


That last command shouldn't involve index groups at all. Since it also 
break more catastrophically with a space in the filename, I'm guessing 
you've reconstructed what you thought you gave as a command.


Don't.

Computers are literal, and so you should be cutting and pasting your 
exact input and output. Making us guess wastes everybody's time.


Probably you used an -s flag, and the index group you chose is larger 
than the size of the atom set in your trajectory. Compare the contents 
of xtc-groups in your .mdp file with this group you chose with trjconv.


Mark
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[gmx-users] regarding rmsd !!

2008-06-17 Thread Anamika Awasthi 
Dear All,
My protein is simulating for 20 ns and 16 ns has already over, but I
want to analyze RMSD and RMSF for this 16 ns simulation, without stopping
the running simulation.it was crashed before, so I used tpbconv -f
previous.trr -e previous.edr -s previous.tpr -o new.tpr -until 2
 then gave the command -->
 mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr

now job is running

now for analysis I am giving this command
g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr

it is giving this output
:-)  g_rms  (-:

Option Filename  Type Description

  -s  topol.tpr  InputStructure+mass(db): tpr tpb tpa gro g96
pdb xml
  -f   new.trr  Input   Generic trajectory: xtc trr t  pdb
 -f2   traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro g96
pdb
  -n  index.ndx  Input, Opt.  Index file
  -o   new_rmsd.xvg  Output   xvgr/xmgr file
-mirrmsdmir.xvg  Output, Opt. xvgr/xmgr file
  -a  avgrp.xvg  Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg  Output, Opt. xvgr/xmgr file
  -m   rmsd.xpm  Output, Opt. X PixMap compatible matrix file
-bin   rmsd.dat  Output, Opt. Generic data file
 -bm   bond.xpm  Output, Opt. X PixMap compatible matrix file

  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
  -[no]X   bool no  Use dialog box GUI to edit command line options
   -niceint 19  Set the nicelevel
  -b   time  0  First frame (ps) to read from trajectory
  -e   time  0  Last frame (ps) to read from trajectory
 -dt   time  0  Only use frame when t MOD dt = first time (ps)
 -tu   enum ps  Time unit: ps, fs, ns, us, ms, s, m or h
  -[no]w   bool no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   boolyes  Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
   -what   enum   rmsd  Structural difference measure: rmsd, rho or
rhosc
-[no]pbc   boolyes  PBC check
-fit   enum rot+trans  Fit to reference structure: rot+trans,
translation or none
   -prevint  0  Compare with previous frame
  -[no]split   bool no  Split graph where time is zero
   -skipint  1  Only write every nr-th frame to matrix
  -skip2int  1  Only write every nr-th frame to matrix
-max   real -1  Maximum level in comparison matrix
-min   real -1  Minimum level in comparison matrix
   -bmax   real -1  Maximum level in bond angle matrix
   -bmin   real -1  Minimum level in bond angle matrix
-nlevelsint 80  Number of levels in the matrices
 -ngint  1  Number of groups to compute RMS between

---
Program g_rms, VERSION 3.3
Source code file: statutil.c, line: 787

Invalid command line argument:
new.tpr
---

 WHY THIS IS SHOWING THIS ERROR?


Thanks in advance

 Anamika
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Re: [gmx-users] regarding rmsd !!

2008-06-17 Thread Per Larsson 

Check your input/output!
In this case it seems you are missing/forgetting the -s flag to  
specify the name of the tpr-file.


/Per




17 jun 2008 kl. 17.07 skrev Anamika Awasthi:




Dear All,
My protein is simulating for 20 ns and 16 ns has already  
over, but I want to analyze RMSD and RMSF for this 16 ns simulation,  
without stopping the running simulation.it was crashed before, so I  
used tpbconv -f  previous.trr -e previous.edr -s previous.tpr -o  
new.tpr -until 2

 then gave the command -->
 mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr

now job is running

now for analysis I am giving this command
g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr

it is giving this output
:-)  g_rms  (-:

Option Filename  Type Description

  -s  topol.tpr  InputStructure+mass(db): tpr tpb tpa  
gro g96 pdb xml

  -f   new.trr  Input   Generic trajectory: xtc trr t  pdb
 -f2   traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj  
gro g96 pdb

  -n  index.ndx  Input, Opt.  Index file
  -o   new_rmsd.xvg  Output   xvgr/xmgr file
-mirrmsdmir.xvg  Output, Opt. xvgr/xmgr file
  -a  avgrp.xvg  Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg  Output, Opt. xvgr/xmgr file
  -m   rmsd.xpm  Output, Opt. X PixMap compatible matrix file
-bin   rmsd.dat  Output, Opt. Generic data file
 -bm   bond.xpm  Output, Opt. X PixMap compatible matrix file

  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
  -[no]X   bool no  Use dialog box GUI to edit command line  
options

   -niceint 19  Set the nicelevel
  -b   time  0  First frame (ps) to read from trajectory
  -e   time  0  Last frame (ps) to read from trajectory
 -dt   time  0  Only use frame when t MOD dt = first  
time (ps)

 -tu   enum ps  Time unit: ps, fs, ns, us, ms, s, m or h
  -[no]w   bool no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   boolyes  Add specific codes (legends etc.) in the  
output

xvg files for the xmgrace program
   -what   enum   rmsd  Structural difference measure: rmsd, rho  
or rhosc

-[no]pbc   boolyes  PBC check
-fit   enum rot+trans  Fit to reference structure: rot+trans,
translation or none
   -prevint  0  Compare with previous frame
  -[no]split   bool no  Split graph where time is zero
   -skipint  1  Only write every nr-th frame to matrix
  -skip2int  1  Only write every nr-th frame to matrix
-max   real -1  Maximum level in comparison matrix
-min   real -1  Minimum level in comparison matrix
   -bmax   real -1  Maximum level in bond angle matrix
   -bmin   real -1  Minimum level in bond angle matrix
-nlevelsint 80  Number of levels in the matrices
 -ngint  1  Number of groups to compute RMS between

---
Program g_rms, VERSION 3.3
Source code file: statutil.c, line: 787

Invalid command line argument:
new.tpr
---

 WHY THIS IS SHOWING THIS ERROR?


Thanks in advance

 Anamika

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Re: [gmx-users] regarding rmsd !!

2008-06-17 Thread Jochen Hub 
I would also suggest to use the xtc and not the trr file for analysis. 
The (compressed) xtc is usually written more often than the 
(full-precision) trr.


Jochen

Anamika Awasthi wrote:



Dear All,
My protein is simulating for 20 ns and 16 ns has already over, 
but I want to analyze RMSD and RMSF for this 16 ns simulation, without 
stopping the running simulation.it  was crashed 
before, so I used tpbconv -f  previous.trr -e previous.edr -s 
previous.tpr -o new.tpr -until 2

 then gave the command -->
 mdrun -s new.tpr -o new.trr -c new.gro -g new.log -e new.edr

now job is running

now for analysis I am giving this command
g_rms new.tpr -f new.trr -o new_rmsd.xvg -xvgr

it is giving this output
:-)  g_rms  (-:

Option Filename  Type Description

  -s  topol.tpr  InputStructure+mass(db): tpr tpb tpa gro 
g96 pdb xml

  -f   new.trr  Input   Generic trajectory: xtc trr t  pdb
 -f2   traj.xtc  Input, Opt.  Generic trajectory: xtc trr trj gro 
g96 pdb

  -n  index.ndx  Input, Opt.  Index file
  -o   new_rmsd.xvg  Output   xvgr/xmgr file
-mirrmsdmir.xvg  Output, Opt. xvgr/xmgr file
  -a  avgrp.xvg  Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg  Output, Opt. xvgr/xmgr file
  -m   rmsd.xpm  Output, Opt. X PixMap compatible matrix file
-bin   rmsd.dat  Output, Opt. Generic data file
 -bm   bond.xpm  Output, Opt. X PixMap compatible matrix file

  Option   Type  Value  Description
--
  -[no]h   bool no  Print help info and quit
  -[no]X   bool no  Use dialog box GUI to edit command line 
options

   -niceint 19  Set the nicelevel
  -b   time  0  First frame (ps) to read from trajectory
  -e   time  0  Last frame (ps) to read from trajectory
 -dt   time  0  Only use frame when t MOD dt = first time (ps)
 -tu   enum ps  Time unit: ps, fs, ns, us, ms, s, m or h
  -[no]w   bool no  View output xvg, xpm, eps and pdb files
   -[no]xvgr   boolyes  Add specific codes (legends etc.) in the 
output

xvg files for the xmgrace program
   -what   enum   rmsd  Structural difference measure: rmsd, rho 
or rhosc

-[no]pbc   boolyes  PBC check
-fit   enum rot+trans  Fit to reference structure: rot+trans,
translation or none
   -prevint  0  Compare with previous frame
  -[no]split   bool no  Split graph where time is zero
   -skipint  1  Only write every nr-th frame to matrix
  -skip2int  1  Only write every nr-th frame to matrix
-max   real -1  Maximum level in comparison matrix
-min   real -1  Minimum level in comparison matrix
   -bmax   real -1  Maximum level in bond angle matrix
   -bmin   real -1  Minimum level in bond angle matrix
-nlevelsint 80  Number of levels in the matrices
 -ngint  1  Number of groups to compute RMS between

---
Program g_rms, VERSION 3.3
Source code file: statutil.c, line: 787

Invalid command line argument:
new.tpr
---

 WHY THIS IS SHOWING THIS ERROR?


Thanks in advance

 Anamika



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--

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
 


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Re: [gmx-users] Position Constraint

2008-06-17 Thread Jochen Hub 

Check the "real posres(..." routine in src/gmxlib/bondfree.c

Jochen

Jae Hyun Park wrote:

Dear GROMACS users,

I would like to modify the source code on the position restraint part 
(restraining the atoms in a protein using -DPOSRES). Could anybody let me know 
where (or which subroutine) I can do it?

Best,
Jae H. Park
===
Jae Hyun Park, Ph.D.
Research Scientist
3215 Beckamn Institute
University of Illinois at Urbana-Champaign
405 North Mathews Avenue
Urbana, IL 61801
(Tel) 217-244-4353, (FAX) 217-244-4333
(E-mail) [EMAIL PROTECTED]
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.

  



--

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312
 


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[gmx-users] RMSD graph

2008-06-17 Thread Anamika Awasthi 
Dear All,
   Please tell, what should I predict from this graph?
   I can understand this is normal type of graph.
   Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to
restart this again and again, I used tpbconv for the same.
but now when I was trying to get rmsd plot from my running job..its not
reading the tpr file, which I got from tpbconv , its reading previous tpr
file.
Is it okey?
  Thanks in advance
 Anamika
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Re: [gmx-users] regarding rmsd !!

2008-06-17 Thread Mark Abraham 

Jochen Hub wrote:
I would also suggest to use the xtc and not the trr file for analysis. 
The (compressed) xtc is usually written more often than the 
(full-precision) trr.


Well, if the user set it up that way. If they have done so, they they 
should be able to remember which is better for their analysis :-)


Mark
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Re: [gmx-users] RMSD graph

2008-06-17 Thread Mark Abraham 

Anamika Awasthi wrote:



Dear All,
   Please tell, what should I predict from this graph?


We can't tell from your graph what's happening because you haven't told 
us how you generated it. It's also not our job to do so - it's yours. 
You can go at look at your data at the points that have "interesting" 
behaviour and see what is causing that. We can't.



   I can understand this is normal type of graph.
   Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to 
restart this again and again, I used tpbconv for the same.


but now when I was trying to get rmsd plot from my running job..its not 
reading the tpr file, which I got from tpbconv , its reading previous 
tpr file.


It's doing what you're telling it to do. No more, no less.

If you don't tell us exactly what you were doing and what you were 
trying to do, we can't offer any insight into the failure.



Is it okey?


No. I guess wildly that you need to correct for periodicity effects, see 
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions


Mark
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Re: [Bulk] [gmx-users] RMSD graph

2008-06-17 Thread Yang Ye 
Quite likely, it is due to part of molecule moving "out of box". Also, 
the molecule could be of multiple chain.


So you need to find a way to put the whole molecule in one piece. Try 
various options from trjconv -pbc. If it is DNA, a trick is to define 
one chain as an index group and then center that group.


Regards,
Yang Ye

Anamika Awasthi wrote:



Dear All,
   Please tell, what should I predict from this graph?
   I can understand this is normal type of graph.
   Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to 
restart this again and again, I used tpbconv for the same.
but now when I was trying to get rmsd plot from my running job..its 
not reading the tpr file, which I got from tpbconv , its reading 
previous tpr file.

Is it okey?
  Thanks in advance
 Anamika
  








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