Re: [gmx-users] urea topology for MARTINI (CGMD)

2010-05-11 Thread Luca Mollica 

On 05/11/2010 04:57 PM, XAvier Periole wrote:


On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:

If we follow strictly the parameterization guides, 

these are only guide lines ... no need to follow "strictly" :))


Actually this was the problem: CG seems easy because of a reduced number 
of points, however getting into the thing (I have experience only in FG 
MD) it's easily realizable that misleading representations of molecules 
can be obtained quite straightforwardly ... :)



Urea has to be mapped to only one CG bead (because of reduction from 
4 to 1), but I believe that this would not be able to represent 
properties of the molecule. Instead I would use a 2 beads model or 
try something like it has been done with water, i.e., more than one 
urea molecule to 1 or 2 beads.
This is only an idea! 

Could be good. Need to be tested ... should not be too difficult.


I agree with you: this is what I had in mind.
Honestly speaking, I am looking for a cosolvent molecule for simulating 
a suitable environment unfolded proteins, that are the systems I am 
currently working on also with the help of
experimental techniques (like SAXS, SANS, NMR or fluorescence). Hence, I 
am not interested in unfolding anything (the usage of Martini for 
protein unfolding is not yet an estabilished
field, as far as I have understood) but rather to observe mesoscale 
dynamics of "already" unfolded peptides in solution.
At the moment I have a good topology for FGMD that has been adapted from 
this paper :


A Kirkwood-Buff Derived Force Field for Mixtures of Urea and Water Source
/The Journal Of Physical Chemistry B/ Volume: 107 Issue: 16 (2003-01-01) 
p. 3891-3898.


that has recently be used in this paper

Equilibrium study of protein denaturation by urea.
/The Journal of the American chemical Society/, 2010 Feb 24;132(7): 2338-44.


and that I have implemented adapting the existing urea FFAMBER topology. 
I think the that same experiments reported in the aforementioned paper 
could be used as a benchmark for CGMD,
once implemented ... the test can be hard, the implementation, actually, 
is almost straightforward.




Tell us about your results!!

Did I mention any result? I have none on urea :((


I presume Esteban inteded my ones ... I read this expectation as a "good 
luck" and "enjoy topology making".

:D

In case we will keep in touch.
Cheers

Luca



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Re: [gmx-users] urea topology for MARTINI (CGMD)

2010-05-11 Thread XAvier Periole 


On May 11, 2010, at 4:48 PM, Esteban Gabriel Vega Hissi wrote:


If we follow strictly the parameterization guides,

these are only guide lines ... no need to follow "strictly" :))
Urea has to be mapped to only one CG bead (because of reduction from  
4 to 1), but I believe that this would not be able to represent  
properties of the molecule. Instead I would use a 2 beads model or  
try something like it has been done with water, i.e., more than one  
urea molecule to 1 or 2 beads.

This is only an idea!

Could be good. Need to be tested ... should not be too difficult.

Tell us about your results!!

Did I mention any result? I have none on urea :((


Best

Esteban
--

2010/5/11 XAvier Periole 

There is no Urea topology for Martini FF. Would be very interesting  
to have one!


you need to look for some properties that you be able to reproduce.
have a look at the papers!

Typically you need to find logP (partitioning data) between different
media and and reproduce it using some Martini bead type ... and in
the case of Urea you might need to define a new type ...

XAvier.


On May 11, 2010, at 3:38 PM, Luca Mollica wrote:

Dear all,
I am looking for a urea topology for some CGMD simulations performed  
with the MARTINI FF.
Actually I am planning to design it on my own, but in case at least  
a "source of inspiration" (I have found no papers about the issue)  
would be appreciated.

Cheers,

Luca



--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a  
pack of cigarettes, it's dark, and we're wearing sunglasses.

Jake: Hit it.

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Re: [gmx-users] urea topology for MARTINI (CGMD)

2010-05-11 Thread Esteban Gabriel Vega Hissi 
If we follow strictly the parameterization guides, Urea has to be mapped to
only one CG bead (because of reduction from 4 to 1), but I believe that this
would not be able to represent properties of the molecule. Instead I would
use a 2 beads model or try something like it has been done with water, i.e.,
more than one urea molecule to 1 or 2 beads.
This is only an idea! Tell us about your results!!

Best

Esteban
--

2010/5/11 XAvier Periole 

>
> There is no Urea topology for Martini FF. Would be very interesting to have
> one!
>
> you need to look for some properties that you be able to reproduce.
> have a look at the papers!
>
> Typically you need to find logP (partitioning data) between different
> media and and reproduce it using some Martini bead type ... and in
> the case of Urea you might need to define a new type ...
>
> XAvier.
>
>
> On May 11, 2010, at 3:38 PM, Luca Mollica wrote:
>
>  Dear all,
>> I am looking for a urea topology for some CGMD simulations performed with
>> the MARTINI FF.
>> Actually I am planning to design it on my own, but in case at least a
>> "source of inspiration" (I have found no papers about the issue) would be
>> appreciated.
>> Cheers,
>>
>> Luca
>>
>>
>>
>> --
>>
>> 
>>
>> --
>>
>>
>>
>> Luca Mollica
>> Protein Dynamics and Flexibility by NMR
>> Institut de Biologie Structurale
>> 41 Rue Jules Horowitz
>> Grenoble
>> 38027
>> France
>>
>> E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)
>>
>> Telephone: +33.438783889
>>
>>
>> --
>>
>>
>> Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack
>> of cigarettes, it's dark, and we're wearing sunglasses.
>> Jake: Hit it.
>>
>> (The Blues Brothers)
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
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Re: [gmx-users] urea topology for MARTINI (CGMD)

2010-05-11 Thread XAvier Periole 


There is no Urea topology for Martini FF. Would be very interesting to  
have one!


you need to look for some properties that you be able to reproduce.
have a look at the papers!

Typically you need to find logP (partitioning data) between different
media and and reproduce it using some Martini bead type ... and in
the case of Urea you might need to define a new type ...

XAvier.

On May 11, 2010, at 3:38 PM, Luca Mollica wrote:


Dear all,
I am looking for a urea topology for some CGMD simulations performed  
with the MARTINI FF.
Actually I am planning to design it on my own, but in case at least  
a "source of inspiration" (I have found no papers about the issue)  
would be appreciated.

Cheers,

Luca



--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a  
pack of cigarettes, it's dark, and we're wearing sunglasses.

Jake: Hit it.

(The Blues Brothers)

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[gmx-users] urea topology for MARTINI (CGMD)

2010-05-11 Thread Luca Mollica 

Dear all,
I am looking for a urea topology for some CGMD simulations performed 
with the MARTINI FF.
Actually I am planning to design it on my own, but in case at least a 
"source of inspiration" (I have found no papers about the issue) would 
be appreciated.

Cheers,

Luca



--



--



Luca Mollica
Protein Dynamics and Flexibility by NMR
Institut de Biologie Structurale
41 Rue Jules Horowitz
Grenoble
38027
France

E-mail: luca.moll...@ibs.fr (lucamoll...@gmail.com)

Telephone: +33.438783889


--


Elwood: It's 106 miles to Chicago, we got a full tank of gas, half a pack of 
cigarettes, it's dark, and we're wearing sunglasses.
Jake: Hit it.

(The Blues Brothers)

--
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Re: [gmx-users] Urea Topology

2009-11-18 Thread TJ Piggot 
They are published in the paper by smith et al. (J. Phys. Chem. B 2004, 
108, 1065-1071) and have also been posted previously on this mailing list 
(both of which can be found through a simple search). Please note that the 
parameters posted on the mailing list are not quite correct as they have 
they have the force constant for the impropers in kJ/mol/deg^2 not in 
kJ/mol/rad^2.


Cheers

Tom

--On Tuesday, November 17, 2009 07:49:01 -0500 "Justin A. Lemkul" 
 wrote:





karan syal wrote:

Dear All,

I am looking for urea topology* (smith et al) *for gromos 96 force
field. I tried searching through user contributions in gromacs site but
couldnt find it. Is it possible for anyone who has already used it to
mail me their toplogy file?



If the parameters are published, you should probably contact the
corresponding author to see if they will share.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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--
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.

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Re: [gmx-users] Urea Topology

2009-11-17 Thread Justin A. Lemkul 



karan syal wrote:

Dear All,

I am looking for urea topology* (smith et al) *for gromos 96 force 
field. I tried searching through user contributions in gromacs site but 
couldnt find it. Is it possible for anyone who has already used it to 
mail me their toplogy file?




If the parameters are published, you should probably contact the corresponding 
author to see if they will share.


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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[gmx-users] Urea Topology

2009-11-17 Thread karan syal 
Dear All,

I am looking for urea topology* (smith et al) *for gromos 96 force field. I
tried searching through user contributions in gromacs site but couldnt find
it. Is it possible for anyone who has already used it to mail me their
toplogy file?
-- 
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Re: [gmx-users] Urea topology problem

2008-12-19 Thread David van der Spoel 

Rebeca García Fandiño wrote:
OK, including a mass colum, as Justin A. Lemkul suggested, worked well. 
Now grompp does not give errors.
Why should I not use this model for urea? I have found also another 
model in the contributions section, for a urea/water box 10M, but why 
should I trust more in a user contribution than in a *itp included in 
Gromacs?
It is your responsibility to choose the right force field for the job, 
hence you have to read the literature.


Maybe we should remove those itp file that are not coupled to a 
published force field.




I don´t have much experience with Gromacs, so any coment will be wellcome.
Thank you very much for your help and suggestions.
Best wishes,
 
Rebeca García

Parc Cientific de Barcelona
rega...@hotmail.com <mailto:rega...@hotmail.com>

 > Date: Thu, 18 Dec 2008 19:50:03 +0100
 > From: sp...@xray.bmc.uu.se
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Urea topology problem
 >
 > Rebeca García Fandiño wrote:
 > > Hello,
 > > I don´t understand the correction I should do from itp.
 > > I have removed from the urea original urea.itp these lines,
 >
 > don't use this model. do a proper literature search.
 >
 > >
 > > #ifdef Boek
 > > 1 C 1 UREA C1 1 0.38
 > > 2 O 1 UREA O2 1 -0.38
 > > 3 NT 1 UREA N3 2 -0.83
 > > 4 H 1 UREA H4 2 0.415
 > > 5 H 1 UREA H5 2 0.415
 > > 6 NT 1 UREA N6 3 -0.83
 > > 7 H 1 UREA H7 3 0.415
 > > 8 H 1 UREA H8 3 0.415
 > > #else
 > > #endif[ moleculetype ]
 > >
 > > so now, my urea.itp file is:
 > >
 > > ; name nrexcl
 > > Urea 3
 > > [ atoms ]
 > > ; nr type resnr residu atom cgnr charge
 > > 1 C 1 UREA C1 1 0.683
 > > 2 O 1 UREA O2 1 -0.683
 > > 3 NT 1 UREA N3 2 -0.622
 > > 4 H 1 UREA H4 2 0.346
 > > 5 H 1 UREA H5 2 0.276
 > > 6 NT 1 UREA N6 3 -0.622
 > > 7 H 1 UREA H7 3 0.346
 > > 8 H 1 UREA H8 3 0.276
 > > [ bonds ]
 > > ; ai aj funct b0 kb
 > > 3 4 1 1.00e-01 3.744680e+05
 > > 3 5 1 1.00e-01 3.744680e+05
 > > 6 7 1 1.00e-01 3.744680e+05
 > > 6 8 1 1.00e-01 3.744680e+05
 > > 1 2 1 1.23e-01 5.020800e+05
 > > 1 3 1 1.33e-01 3.765600e+05
 > > 1 6 1 1.33e-01 3.765600e+05
 > > [ pairs ]
 > > ; ai aj funct c6 c12
 > > 2 4 1 0.00e+00 0.00e+00
 > > 2 5 1 0.00e+00 0.00e+00
 > > 2 7 1 0.00e+00 0.00e+00
 > > 2 8 1 0.00e+00 0.00e+00
 > > 3 7 1 0.00e+00 0.00e+00
 > > 3 8 1 0.00e+00 0.00e+00
 > > 4 6 1 0.00e+00 0.00e+00
 > > 5 6 1 0.00e+00 0.00e+00
 > > [ angles ]
 > > ; ai aj ak funct th0 cth
 > > 1 3 4 1 1.20e+02 2.928800e+02
 > > 1 3 5 1 1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02
 > > 3 1 6 1 1.17e+02 5.020800e+02
 > > [ dihedrals ]
 > > ; ai aj ak al funct phi cp mult
 > > 2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00
 > > 6 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00
 > > 2 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00
 > > 6 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00
 > > 2 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00
 > > 3 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00
 > > 2 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00
 > > 3 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00
 > > [ dihedrals ]
 > > ; ai aj ak al funct q0 cq
 > > 3 4 5 1 2 0.00e+00 1.673600e+02
 > > 6 7 8 1 2 0.00e+00 1.673600e+02
 > > 1 3 6 2 2 0.00e+00 1.673600e+02
 > >
 > > 4 3 5 1 1.20e+02 3.347200e+02
 > > 1 6 7 1 1.20e+02 2.928800e+02
 > > 1 6 8 1 1.20e+02 2.928800e+02
 > > 7 6 8 1 1.20e+02 3.347200e+02
 > > 2 1 3 1 1.215000e+02 5.020800e+02
 > >
 > >
 > > Following Chapter 5 in the manual (page 102), the file described for
 > > urea.itp is the same as mine. For the topology (page 103)
 > > #include "ffgmx.itp" is used, but I don´t see any more different.
 > > With this modification in the urea.itp I get the same error. Any 
idea of

 > > what could be the problem?
 > > Thank you very much for your help,
 > >
 > > Rebeca Garcia
 > > Parc Cientific de Barcelona
 > > rega...@hotmail.com <mailto:rega...@hotmail.com>
 > >
 > >
 > >
 > >
 > >
 > > > Date: Thu, 18 Dec 2008 09:21:41 -0500
 > > > From: jalem...@vt.edu
 > > > To: gmx-users@gromacs.org
 > > > Subject: Re: [gmx-users] Urea topology problem
 > > >
 > > >
 > > >
 > > > Rebeca García Fandiño wrote:
 > > >
 > > > 
 > > >
 > > > >
 > >

RE: [gmx-users] Urea topology problem

2008-12-19 Thread Rebeca García Fandiño 

OK, including a mass colum, as Justin A. Lemkul suggested, worked well. Now 
grompp does not give errors.
Why should I not use this model for urea? I have found also another model in 
the contributions section, for a urea/water box 10M, but why should I trust 
more in a user contribution than in a *itp included in Gromacs?
I don´t have much experience with Gromacs, so any coment will be wellcome. 
Thank you very much for your help and suggestions.
Best wishes,
 
Rebeca García 
Parc Cientific de Barcelona
rega...@hotmail.com> Date: Thu, 18 Dec 2008 19:50:03 +0100> From: 
sp...@xray.bmc.uu.se> To: gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea 
topology problem> > Rebeca García Fandiño wrote:> > Hello,> > I don´t 
understand the correction I should do from itp.> > I have removed from the urea 
original urea.itp these lines,> > don't use this model. do a proper literature 
search.> > > > > #ifdef Boek> > 1 C 1 UREA C1 1 0.38> > 2 O 1 UREA O2 1 -0.38> 
> 3 NT 1 UREA N3 2 -0.83> > 4 H 1 UREA H4 2 0.415> > 5 H 1 UREA H5 2 0.415> > 6 
NT 1 UREA N6 3 -0.83> > 7 H 1 UREA H7 3 0.415> > 8 H 1 UREA H8 3 0.415> > 
#else> > #endif[ moleculetype ]> > > > so now, my urea.itp file is:> > > > ; 
name nrexcl> > Urea 3> > [ atoms ]> > ; nr type resnr residu atom cgnr charge> 
> 1 C 1 UREA C1 1 0.683> > 2 O 1 UREA O2 1 -0.683> > 3 NT 1 UREA N3 2 -0.622> > 
4 H 1 UREA H4 2 0.346> > 5 H 1 UREA H5 2 0.276> > 6 NT 1 UREA N6 3 -0.622> > 7 
H 1 UREA H7 3 0.346> > 8 H 1 UREA H8 3 0.276> > [ bonds ]> > ; ai aj funct b0 
kb> > 3 4 1 1.00e-01 3.744680e+05> > 3 5 1 1.00e-01 3.744680e+05> > 6 7 
1 1.00e-01 3.744680e+05> > 6 8 1 1.00e-01 3.744680e+05> > 1 2 1 
1.23e-01 5.020800e+05> > 1 3 1 1.33e-01 3.765600e+05> > 1 6 1 
1.33e-01 3.765600e+05> > [ pairs ]> > ; ai aj funct c6 c12> > 2 4 1 
0.00e+00 0.00e+00> > 2 5 1 0.00e+00 0.00e+00> > 2 7 1 
0.00e+00 0.00e+00> > 2 8 1 0.00e+00 0.00e+00> > 3 7 1 
0.00e+00 0.00e+00> > 3 8 1 0.00e+00 0.00e+00> > 4 6 1 
0.00e+00 0.00e+00> > 5 6 1 0.00e+00 0.00e+00> > [ angles ]> > ; 
ai aj ak funct th0 cth> > 1 3 4 1 1.20e+02 2.928800e+02> > 1 3 5 1 
1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02> > 3 1 6 1 
1.17e+02 5.020800e+02> > [ dihedrals ]> > ; ai aj ak al funct phi cp mult> 
> 2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00> > 6 1 3 4 1 1.80e+02 
3.347200e+01 2.00e+00> > 2 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00> 
> 6 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00> > 2 1 6 7 1 1.80e+02 
3.347200e+01 2.00e+00> > 3 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00> 
> 2 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00> > 3 1 6 8 1 1.80e+02 
3.347200e+01 2.00e+00> > [ dihedrals ]> > ; ai aj ak al funct q0 cq> > 3 4 
5 1 2 0.00e+00 1.673600e+02> > 6 7 8 1 2 0.00e+00 1.673600e+02> > 1 3 6 
2 2 0.00e+00 1.673600e+02> > > > 4 3 5 1 1.20e+02 3.347200e+02> > 1 6 7 
1 1.20e+02 2.928800e+02> > 1 6 8 1 1.20e+02 2.928800e+02> > 7 6 8 1 
1.20e+02 3.347200e+02> > 2 1 3 1 1.215000e+02 5.020800e+02> > > > > > 
Following Chapter 5 in the manual (page 102), the file described for > > 
urea.itp is the same as mine. For the topology (page 103)> > #include 
"ffgmx.itp" is used, but I don´t see any more different.> > With this 
modification in the urea.itp I get the same error. Any idea of > > what could 
be the problem?> > Thank you very much for your help,> > > > Rebeca Garcia > > 
Parc Cientific de Barcelona> > rega...@hotmail.com 
<mailto:rega...@hotmail.com>> > > > > > > > > > > > > Date: Thu, 18 Dec 2008 
09:21:41 -0500> > > From: jalem...@vt.edu> > > To: gmx-users@gromacs.org> > > 
Subject: Re: [gmx-users] Urea topology problem> > >> > >> > >> > > Rebeca 
García Fandiño wrote:> > >> > > > > >> > > >> > > > ERROR 1 [file 
solvated.top, line 39]:> > > >> > > > atom C1 (Res UREA-1) has mass 0> > > >> > 
> >> > >> > > In urea.itp, no masses are defined. If you correct the format of 
this > > file (see> > > Chapter 5 of the manual), then this issue should be 
resolved.> > >> > >> > > >> > > > Which force field does

Re: [gmx-users] Urea topology problem

2008-12-18 Thread David van der Spoel 

Rebeca García Fandiño wrote:

Hello,
I don´t understand the correction I should do from itp.
I have removed from the urea original urea.itp these lines,


don't use this model. do a proper literature search.

 
#ifdef Boek

 1   C   1UREA  C1   1   0.38
 2   O   1UREA  O2   1  -0.38
 3  NT   1UREA  N3   2  -0.83
 4   H   1UREA  H4   2   0.415
 5   H   1UREA  H5   2   0.415
 6  NT   1UREA  N6   3  -0.83
 7   H   1UREA  H7   3   0.415
 8   H   1UREA  H8   3   0.415
#else
 #endif[ moleculetype ]
 
so now, my urea.itp file is:


; name nrexcl
Urea 3
[ atoms ]
; nr type resnr residu atom cgnr charge
1 C 1 UREA C1 1 0.683
2 O 1 UREA O2 1 -0.683
3 NT 1 UREA N3 2 -0.622
4 H 1 UREA H4 2 0.346
5 H 1 UREA H5 2 0.276
6 NT 1 UREA N6 3 -0.622
7 H 1 UREA H7 3 0.346
8 H 1 UREA H8 3 0.276
[ bonds ]
; ai aj funct b0 kb
3 4 1 1.00e-01 3.744680e+05
3 5 1 1.00e-01 3.744680e+05
6 7 1 1.00e-01 3.744680e+05
6 8 1 1.00e-01 3.744680e+05
1 2 1 1.23e-01 5.020800e+05
1 3 1 1.33e-01 3.765600e+05
1 6 1 1.33e-01 3.765600e+05
[ pairs ]
; ai aj funct c6 c12
2 4 1 0.00e+00 0.00e+00
2 5 1 0.00e+00 0.00e+00
2 7 1 0.00e+00 0.00e+00
2 8 1 0.00e+00 0.00e+00
3 7 1 0.00e+00 0.00e+00
3 8 1 0.00e+00 0.00e+00
4 6 1 0.00e+00 0.00e+00
5 6 1 0.00e+00 0.00e+00
[ angles ]
; ai aj ak funct th0 cth
1 3 4 1 1.20e+02 2.928800e+02
1 3 5 1 1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+02
3 1 6 1 1.17e+02 5.020800e+02
[ dihedrals ]
; ai aj ak al funct phi cp mult
2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00
6 1 3 4 1 1.80e+02 3.347200e+01 2.00e+00
2 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00
6 1 3 5 1 1.80e+02 3.347200e+01 2.00e+00
2 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00
3 1 6 7 1 1.80e+02 3.347200e+01 2.00e+00
2 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00
3 1 6 8 1 1.80e+02 3.347200e+01 2.00e+00
[ dihedrals ]
; ai aj ak al funct q0 cq
3 4 5 1 2 0.00e+00 1.673600e+02
6 7 8 1 2 0.00e+00 1.673600e+02
1 3 6 2 2 0.00e+00 1.673600e+02

4 3 5 1 1.20e+02 3.347200e+02
1 6 7 1 1.20e+02 2.928800e+02
1 6 8 1 1.20e+02 2.928800e+02
7 6 8 1 1.20e+02 3.347200e+02
2 1 3 1 1.215000e+02 5.020800e+02

 
Following Chapter 5 in the manual (page 102), the file described for 
urea.itp is the same as mine. For the topology (page 103)

#include "ffgmx.itp" is used, but I don´t see any more different.
With this modification in the urea.itp I get the same error. Any idea of 
what could be the problem?

Thank you very much for your help,
 
 Rebeca Garcia 
Parc Cientific de Barcelona

 rega...@hotmail.com <mailto:rega...@hotmail.com>


 



 > Date: Thu, 18 Dec 2008 09:21:41 -0500
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Urea topology problem
 >
 >
 >
 > Rebeca García Fandiño wrote:
 >
 > 
 >
 > >
 > > ERROR 1 [file solvated.top, line 39]:
 > >
 > > atom C1 (Res UREA-1) has mass 0
 > >
 > >
 >
 > In urea.itp, no masses are defined. If you correct the format of this 
file (see

 > Chapter 5 of the manual), then this issue should be resolved.
 >
 >
 > >
 > > Which force field does this urea.itp correspond to? Where should it 
look

 > > for the atomtypes of urea?
 > >
 > >
 >
 > The .atp file corresponding to the force field you are using 
(ffG43a2). The
 > atomtypes for urea appear to be generic for use with the Gromos96 
force fields.
 > There are specific atomtypes within ffG53a6 for urea, if you want to 
use the

 > newer force field (check the ffG53a6.rtp file for the urea parameters).
 >
 > -Justin
 >
 >
 > >
 > > Thank you very much for your help,
 > >
 > >
 > >
 > > Rebeca Garcia
 > >
 > > Parc Cientific de Barcelona
 > >
 > > rega...@hotmail.com
 > >
 > >
 > > 

 > > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo 
gratis

 > > <http://vivelive.com/ieak7/>
 > >
 > >
 > > 


 > >
 > > ___
 > > 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 gmx-users-requ...@gromacs.org.
 > > Can&#

Re: [gmx-users] Urea topology problem

2008-12-18 Thread Justin A. Lemkul 



Rebeca García Fandiño wrote:

Hello,
I don´t understand the correction I should do from itp.
I have removed from the urea original urea.itp these lines,
 


The error message was that grompp couldn't find masses for these atoms.  The 
correct format should include a mass column after the charge column (see, for 
example, your protein topology from pdb2gmx).  I guess the manual needs a bit of 
revision.




Following Chapter 5 in the manual (page 102), the file described for 
urea.itp is the same as mine. For the topology (page 103)

#include "ffgmx.itp" is used, but I don´t see any more different.
With this modification in the urea.itp I get the same error. Any idea of 
what could be the problem?


As a general warning, don't use ffgmx.  It is deprecated.  Stick with Gromos96, 
as you had initially intended.


-Justin


Thank you very much for your help,
 
 Rebeca Garcia 
Parc Cientific de Barcelona

 rega...@hotmail.com <mailto:rega...@hotmail.com>


 



 > Date: Thu, 18 Dec 2008 09:21:41 -0500
 > From: jalem...@vt.edu
 > To: gmx-users@gromacs.org
 > Subject: Re: [gmx-users] Urea topology problem
 >
 >
 >
 > Rebeca García Fandiño wrote:
 >
 > 
 >
 > >
 > > ERROR 1 [file solvated.top, line 39]:
 > >
 > > atom C1 (Res UREA-1) has mass 0
 > >
 > >
 >
 > In urea.itp, no masses are defined. If you correct the format of this 
file (see

 > Chapter 5 of the manual), then this issue should be resolved.
 >
 >
 > >
 > > Which force field does this urea.itp correspond to? Where should it 
look

 > > for the atomtypes of urea?
 > >
 > >
 >
 > The .atp file corresponding to the force field you are using 
(ffG43a2). The
 > atomtypes for urea appear to be generic for use with the Gromos96 
force fields.
 > There are specific atomtypes within ffG53a6 for urea, if you want to 
use the

 > newer force field (check the ffG53a6.rtp file for the urea parameters).
 >
 > -Justin
 >
 >
 > >
 > > Thank you very much for your help,
 > >
 > >
 > >
 > > Rebeca Garcia
 > >
 > > Parc Cientific de Barcelona
 > >
 > > rega...@hotmail.com
 > >
 > >
 > > 

 > > ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo 
gratis

 > > <http://vivelive.com/ieak7/>
 > >
 > >
 > > 


 > >
 > > ___
 > > 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 gmx-users-requ...@gromacs.org.
 > > 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 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 gmx-users-requ...@gromacs.org.
 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php



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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


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RE: [gmx-users] Urea topology problem

2008-12-18 Thread Rebeca García Fandiño 

Hello,
I don´t understand the correction I should do from itp. 
I have removed from the urea original urea.itp these lines,
 
#ifdef Boek 1   C   1UREA  C1   1   0.38 2   O  
 1UREA  O2   1  -0.38 3  NT   1UREA  N3 
  2  -0.83 4   H   1UREA  H4   2   0.415 5   H  
 1UREA  H5   2   0.415 6  NT   1UREA  N6
   3  -0.83 7   H   1UREA  H7   3   0.415 8   H 
  1UREA  H8   3   0.415#else #endif[ moleculetype ]
 
so now, my urea.itp file is:
; name nrexclUrea 3
[ atoms ]; nr type resnr residu atom cgnr charge1 C 1 UREA C1 1 0.6832 O 1 UREA 
O2 1 -0.6833 NT 1 UREA N3 2 -0.6224 H 1 UREA H4 2 0.3465 H 1 UREA H5 2 0.2766 
NT 1 UREA N6 3 -0.6227 H 1 UREA H7 3 0.3468 H 1 UREA H8 3 0.276
[ bonds ]; ai aj funct b0 kb3 4 1 1.00e-01 3.744680e+053 5 1 1.00e-01 
3.744680e+056 7 1 1.00e-01 3.744680e+056 8 1 1.00e-01 3.744680e+051 2 1 
1.23e-01 5.020800e+051 3 1 1.33e-01 3.765600e+051 6 1 1.33e-01 
3.765600e+05
[ pairs ]; ai aj funct c6 c122 4 1 0.00e+00 0.00e+002 5 1 0.00e+00 
0.00e+002 7 1 0.00e+00 0.00e+002 8 1 0.00e+00 0.00e+003 7 1 
0.00e+00 0.00e+003 8 1 0.00e+00 0.00e+004 6 1 0.00e+00 
0.00e+005 6 1 0.00e+00 0.00e+00
[ angles ]; ai aj ak funct th0 cth1 3 4 1 1.20e+02 2.928800e+021 3 5 1 
1.20e+02 2.928800e+022 1 6 1 1.215000e+02 5.020800e+023 1 6 1 1.17e+02 
5.020800e+02
[ dihedrals ]; ai aj ak al funct phi cp mult
2 1 3 4 1 1.80e+02 3.347200e+01 2.00e+006 1 3 4 1 1.80e+02 
3.347200e+01 2.00e+002 1 3 5 1 1.80e+02 3.347200e+01 2.00e+006 1 3 
5 1 1.80e+02 3.347200e+01 2.00e+002 1 6 7 1 1.80e+02 3.347200e+01 
2.00e+003 1 6 7 1 1.80e+02 3.347200e+01 2.00e+002 1 6 8 1 
1.80e+02 3.347200e+01 2.00e+003 1 6 8 1 1.80e+02 3.347200e+01 
2.00e+00
[ dihedrals ]; ai aj ak al funct q0 cq3 4 5 1 2 0.00e+00 1.673600e+026 7 8 
1 2 0.00e+00 1.673600e+021 3 6 2 2 0.00e+00 1.673600e+024 3 5 1 
1.20e+02 3.347200e+021 6 7 1 1.20e+02 2.928800e+021 6 8 1 1.20e+02 
2.928800e+027 6 8 1 1.20e+02 3.347200e+022 1 3 1 1.215000e+02 5.020800e+02
 
Following Chapter 5 in the manual (page 102), the file described for urea.itp 
is the same as mine. For the topology (page 103) 
#include "ffgmx.itp" is used, but I don´t see any more different. 
With this modification in the urea.itp I get the same error. Any idea of what 
could be the problem?
Thank you very much for your help,
 
 Rebeca Garcia  Parc Cientific de Barcelona rega...@hotmail.com
 
> Date: Thu, 18 Dec 2008 09:21:41 -0500> From: jalem...@vt.edu> To: 
> gmx-users@gromacs.org> Subject: Re: [gmx-users] Urea topology problem> > > > 
> Rebeca García Fandiño wrote:> > > > > > > ERROR 1 [file solvated.top, 
> line 39]:> > > > atom C1 (Res UREA-1) has mass 0> > > > > > In urea.itp, no 
> masses are defined. If you correct the format of this file (see > Chapter 5 
> of the manual), then this issue should be resolved.> > > > > > Which force 
> field does this urea.itp correspond to? Where should it look > > for the 
> atomtypes of urea?> > > >> > The .atp file corresponding to the force field 
> you are using (ffG43a2). The > atomtypes for urea appear to be generic for 
> use with the Gromos96 force fields. > There are specific atomtypes within 
> ffG53a6 for urea, if you want to use the > newer force field (check the 
> ffG53a6.rtp file for the urea parameters).> > -Justin> > > > > > Thank you 
> very much for your help,> > > > > > > > Rebeca Garcia> > > > Parc Cientific 
> de Barcelona> > > > rega...@hotmail.com> > > > > > 
> > > 
> ¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo gratis > > 
> <http://vivelive.com/ieak7/>> > > > > > 
> > > > 
> > ___> > 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 gmx-users-requ...@gromacs.org.> > Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php> > -- > 
> > > Justin A. Lemkul> Graduate

Re: [gmx-users] Urea topology problem

2008-12-18 Thread Justin A. Lemkul 



Rebeca García Fandiño wrote:





ERROR 1 [file solvated.top, line 39]:

  atom C1 (Res UREA-1) has mass 0

 


In urea.itp, no masses are defined.  If you correct the format of this file (see 
Chapter 5 of the manual), then this issue should be resolved.





Which force field does this urea.itp correspond to? Where should it look 
for the atomtypes of urea?





The .atp file corresponding to the force field you are using (ffG43a2).  The 
atomtypes for urea appear to be generic for use with the Gromos96 force fields. 
 There are specific atomtypes within ffG53a6 for urea, if you want to use the 
newer force field (check the ffG53a6.rtp file for the urea parameters).


-Justin




Thank you very much for your help,

 


Rebeca Garcia

Parc Cientific de Barcelona

rega...@hotmail.com



¿Aún no tienes Internet Explorer 7? Bájatelo y consigue un regalo gratis 






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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


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[gmx-users] Urea topology problem

2008-12-18 Thread Rebeca García Fandiño 

Hello,
I would like to simulate a proteína in urea, using Gromacs. I have tried to use 
the box included in Gromacs by default (urea+h2o.gro and urea.itp). 
The topology of the urea/water-solvated protein is:
 

; Include forcefield parameters
#include "ffG43a2.itp"

#include "protein.itp"
 

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
 
; Include water and urea topology
#include "urea.itp"
#include "spc.itp"
 
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif
 
[ system ]
; Name
Protein in water/urea
 
[ molecules ]
; Compound#mols
Protein 1
UREA426
SOL 5885
 
 When I try
 grompp -f min.mdp -c solvated_urea.gro -p solvated.top -o min.tpr
 
I get these errors:
 
ERROR 1 [file solvated.top, line 39]:
  atom C1 (Res UREA-1) has mass 0
 
ERROR 2 [file solvated.top, line 39]:
  atom O2 (Res UREA-1) has mass 0
 
ERROR 3 [file solvated.top, line 39]:
  atom N3 (Res UREA-1) has mass 0
 
ERROR 4 [file solvated.top, line 39]:
  atom H4 (Res UREA-1) has mass 0
 
ERROR 5 [file solvated.top, line 39]:
  atom H5 (Res UREA-1) has mass 0
 
ERROR 6 [file solvated.top, line 39]:
  atom N6 (Res UREA-1) has mass 0
 
ERROR 7 [file solvated.top, line 39]:
  atom H7 (Res UREA-1) has mass 0
 
ERROR 8 [file solvated.top, line 39]:
  atom H8 (Res UREA-1) has mass 0
 
Which force field does this urea.itp correspond to? Where should it look for 
the atomtypes of urea?
 
Thank you very much for your help,
 
Rebeca Garcia
Parc Cientific de Barcelona
rega...@hotmail.com
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