[gmx-users] parameters for Hem ligated with co

[라지브간디]

Dear all,


Can anyone please share your heme ligated to CO ligand parameters? There is a 
parameters file exist in charmm22 and gromos but they are not well defined.


It would be really appreciated if you anyone share here. Thanks.




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[gmx-users] parameters for output control

[mohammad agha]

Dear Mark,

Thank you very much from your help.

Best Regards
Sara




- Original Message -
From: Mark Abraham 
To: Discussion list for GROMACS users 
Cc: 
Sent: Tuesday, August 21, 2012 9:45 AM
Subject: Re: [gmx-users] parameters for output control

On 21/08/2012 2:55 PM, mohammad agha wrote:
> Dear Justin,
>
> Thank you very much from your response. Yes, I said bad!!!
> My question is: For example, when I select -b 8 and Gromacs reads as (in 
> the last step of reading from output file): Reading frame 13000 time 
> 860040.000 , does it perform the computation untill time= 860040 ps or not? 
> or does Gromacs perform the computations untill end of simulation (90 ps) 
> and only doesn't printe in the command line?

You asked for everything after time 8, and that's what you got. If 
you really want to be sure, use trjconv to make the subset of the 
trajectory, verify its content with gmxcheck or gmxdump, and use g_rdf 
on that. And then observe you get the same result as you already have.

Mark

>
> Best Reagrds
> Sara
> - Original Message -
> From: Justin Lemkul 
> To: mohammad agha ; Discussion list for GROMACS users 
> 
> Cc:
> Sent: Monday, August 20, 2012 10:45 AM
> Subject: Re: [gmx-users] parameters for output control
>
>
>
> On 8/20/12 1:15 PM, mohammad agha wrote:
>> Dear Gromacs Users,
>>
>> I have one problem about the way of computation in the Gromacs with frame 
>> and time. (I work with MARTINI CG)
>> I have one md.mdp file that the parameters of output control in it is as 
>> follows:
>> nsteps = 3000
>> dt = 0.030
>> ; Output control
>> nstxout = 2000
>> nstvout = 2000
>> nstenergy = 2000
>> nstlog = 2000
>> nstxtcout = 2000
>> xtc_precision = 1000
>> Consequently, total time of my system is 90 ps.When I want to obtaine 
>> some information about my system for example RDF by g_rdf command, 
>> computation of Gromacs perfome as follows:
>> Reading frame 200 time 12000.000
>> .300
>> .400
>> .500
>> .600
>> .700
>> ...
>> ...
>> ...
>> Reading frame 2000 time 12.000
>> .3000
>> .4000
>> .5000
>> .6000
>> .7000
>> ...
>> ...
>> ...
>> Last frame 15000 time 90.000
>> It means that until frame 2000 reading is 100 to 100 in frames and from 2000 
>> to end, it is 1000 to 1000.
> I don't understand this assertion.  You have frames every 60 ps, as expected. 
> Console output is buffered so that the programs are not wasting time 
> continually updating the frame number and time value.
>
>> Also, I did with this parameters:
>> ; Output control
>> nstxout = 200
>> nstvout = 200
>> nstenergy = 100
>> nstlog = 200
>> nstxtcout = 200
>> xtc_precision = 100
>> but the result of reading the frames was the same previous.
>> I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find 
>> problem when I use -b in g_rdf command. for eaxample, with -b 8, reading 
>> is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end 
>> of simulation (90).
> This sounds like the same issue above.  The console output may be incomplete. 
> It's merely a convenience to have an estimate of how long the calculation is 
> taking.
>
>> Also, I want to have smaller systems with smaller volume by convert 2000 to 
>> 1 for parameters for output control but I want reading from frame for 
>> computation of properties become 100 frames to 100 frames or 10 frames to 10 
>> frames.
>>
> I also don't understand this statement so I can't offer anything to 
> particularly useful to help.
>
> -Justin
>
> -- 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] parameters for output control

[Mark Abraham]

On 21/08/2012 2:55 PM, mohammad agha wrote:

Dear Justin,

Thank you very much from your response. Yes, I said bad!!!
My question is: For example, when I select -b 8 and Gromacs reads as (in 
the last step of reading from output file): Reading frame 13000 time 860040.000 
, does it perform the computation untill time= 860040 ps or not? or does 
Gromacs perform the computations untill end of simulation (90 ps) and only 
doesn't printe in the command line?


You asked for everything after time 8, and that's what you got. If 
you really want to be sure, use trjconv to make the subset of the 
trajectory, verify its content with gmxcheck or gmxdump, and use g_rdf 
on that. And then observe you get the same result as you already have.


Mark



Best Reagrds
Sara
- Original Message -
From: Justin Lemkul 
To: mohammad agha ; Discussion list for GROMACS users 

Cc:
Sent: Monday, August 20, 2012 10:45 AM
Subject: Re: [gmx-users] parameters for output control



On 8/20/12 1:15 PM, mohammad agha wrote:

Dear Gromacs Users,

I have one problem about the way of computation in the Gromacs with frame and 
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as 
follows:
nsteps = 3000
dt = 0.030
; Output control
nstxout = 2000
nstvout = 2000
nstenergy = 2000
nstlog = 2000
nstxtcout = 2000
xtc_precision = 1000
Consequently, total time of my system is 90 ps.When I want to obtaine some 
information about my system for example RDF by g_rdf command, computation of 
Gromacs perfome as follows:
Reading frame 200 time 12000.000
.300
.400
.500
.600
.700
...
...
...
Reading frame 2000 time 12.000
.3000
.4000
.5000
.6000
.7000
...
...
...
Last frame 15000 time 90.000
It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to 
end, it is 1000 to 1000.

I don't understand this assertion.  You have frames every 60 ps, as expected. 
Console output is buffered so that the programs are not wasting time 
continually updating the frame number and time value.


Also, I did with this parameters:
; Output control
nstxout = 200
nstvout = 200
nstenergy = 100
nstlog = 200
nstxtcout = 200
xtc_precision = 100
but the result of reading the frames was the same previous.
I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find 
problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is 
only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of 
simulation (90).

This sounds like the same issue above.  The console output may be incomplete. 
It's merely a convenience to have an estimate of how long the calculation is 
taking.


Also, I want to have smaller systems with smaller volume by convert 2000 to 
1 for parameters for output control but I want reading from frame for 
computation of properties become 100 frames to 100 frames or 10 frames to 10 
frames.


I also don't understand this statement so I can't offer anything to 
particularly useful to help.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for output control

[mohammad agha]

Dear Justin,

Thank you very much from your response. Yes, I said bad!!!
My question is: For example, when I select -b 8 and Gromacs reads as (in 
the last step of reading from output file): Reading frame 13000 time 860040.000 
, does it perform the computation untill time= 860040 ps or not? or does 
Gromacs perform the computations untill end of simulation (90 ps) and only 
doesn't printe in the command line?

Best Reagrds
Sara 
- Original Message -
From: Justin Lemkul 
To: mohammad agha ; Discussion list for GROMACS users 

Cc: 
Sent: Monday, August 20, 2012 10:45 AM
Subject: Re: [gmx-users] parameters for output control



On 8/20/12 1:15 PM, mohammad agha wrote:
> Dear Gromacs Users,
> 
> I have one problem about the way of computation in the Gromacs with frame and 
> time. (I work with MARTINI CG)
> I have one md.mdp file that the parameters of output control in it is as 
> follows:
> nsteps = 3000
> dt = 0.030
> ; Output control
> nstxout = 2000
> nstvout = 2000
> nstenergy = 2000
> nstlog = 2000
> nstxtcout = 2000
> xtc_precision = 1000
> Consequently, total time of my system is 90 ps.When I want to obtaine 
> some information about my system for example RDF by g_rdf command, 
> computation of Gromacs perfome as follows:
> Reading frame 200 time 12000.000
> .300
> .400
> .500
> .600
> .700
> ...
> ...
> ...
> Reading frame 2000 time 12.000
> .3000
> .4000
> .5000
> .6000
> .7000
> ...
> ...
> ...
> Last frame 15000 time 90.000
> It means that until frame 2000 reading is 100 to 100 in frames and from 2000 
> to end, it is 1000 to 1000.

I don't understand this assertion.  You have frames every 60 ps, as expected. 
Console output is buffered so that the programs are not wasting time 
continually updating the frame number and time value.

> Also, I did with this parameters:
> ; Output control
> nstxout = 200
> nstvout = 200
> nstenergy = 100
> nstlog = 200
> nstxtcout = 200
> xtc_precision = 100
> but the result of reading the frames was the same previous.
> I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find 
> problem when I use -b in g_rdf command. for eaxample, with -b 8, reading 
> is only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end 
> of simulation (90).

This sounds like the same issue above.  The console output may be incomplete. 
It's merely a convenience to have an estimate of how long the calculation is 
taking.

> Also, I want to have smaller systems with smaller volume by convert 2000 to 
> 1 for parameters for output control but I want reading from frame for 
> computation of properties become 100 frames to 100 frames or 10 frames to 10 
> frames.
> 

I also don't understand this statement so I can't offer anything to 
particularly useful to help.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for output control

[Justin Lemkul]

On 8/20/12 1:15 PM, mohammad agha wrote:

Dear Gromacs Users,

I have one problem about the way of computation in the Gromacs with frame and 
time. (I work with MARTINI CG)
I have one md.mdp file that the parameters of output control in it is as 
follows:
nsteps = 3000
dt = 0.030
; Output control
nstxout = 2000
nstvout = 2000
nstenergy = 2000
nstlog = 2000
nstxtcout = 2000
xtc_precision = 1000
Consequently, total time of my system is 90 ps.When I want to obtaine some 
information about my system for example RDF by g_rdf command, computation of 
Gromacs perfome as follows:
Reading frame 200 time 12000.000
.300
.400
.500
.600
.700
...
...
...
Reading frame 2000 time 12.000
.3000
.4000
.5000
.6000
.7000
...
...
...
Last frame 15000 time 90.000
It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to 
end, it is 1000 to 1000.


I don't understand this assertion.  You have frames every 60 ps, as expected. 
Console output is buffered so that the programs are not wasting time continually 
updating the frame number and time value.



Also, I did with this parameters:
; Output control
nstxout = 200
nstvout = 200
nstenergy = 100
nstlog = 200
nstxtcout = 200
xtc_precision = 100
but the result of reading the frames was the same previous.
I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find 
problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is 
only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of 
simulation (90).


This sounds like the same issue above.  The console output may be incomplete. 
It's merely a convenience to have an estimate of how long the calculation is taking.



Also, I want to have smaller systems with smaller volume by convert 2000 to 
1 for parameters for output control but I want reading from frame for 
computation of properties become 100 frames to 100 frames or 10 frames to 10 
frames.



I also don't understand this statement so I can't offer anything to particularly 
useful to help.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[gmx-users] parameters for output control

[mohammad agha]

Dear Gromacs Users, 

I have one problem about the way of computation in the Gromacs with frame and 
time. (I work with MARTINI CG) 
I have one md.mdp file that the parameters of output control in it is as 
follows: 
nsteps = 3000 
dt = 0.030 
; Output control 
nstxout = 2000 
nstvout = 2000 
nstenergy = 2000 
nstlog = 2000 
nstxtcout = 2000 
xtc_precision = 1000 
Consequently, total time of my system is 90 ps.When I want to obtaine some 
information about my system for example RDF by g_rdf command, computation of 
Gromacs perfome as follows: 
Reading frame 200 time 12000.000 
.300 
.400 
.500 
.600 
.700 
... 
... 
... 
Reading frame 2000 time 12.000 
.3000 
.4000 
.5000 
.6000 
.7000 
... 
... 
... 
Last frame 15000 time 90.000 
It means that until frame 2000 reading is 100 to 100 in frames and from 2000 to 
end, it is 1000 to 1000. 
Also, I did with this parameters: 
; Output control 
nstxout = 200 
nstvout = 200 
nstenergy = 100 
nstlog = 200 
nstxtcout = 200 
xtc_precision = 100 
but the result of reading the frames was the same previous. 
I want to Gromacs read frames 100 to 100 not 1000 to 1000, because I find 
problem when I use -b in g_rdf command. for eaxample, with -b 8, reading is 
only until 860040 ps, Reading frame 13000 time 860040.000 ,not until end of 
simulation (90). 
Also, I want to have smaller systems with smaller volume by convert 2000 to 
1 for parameters for output control but I want reading from frame for 
computation of properties become 100 frames to 100 frames or 10 frames to 10 
frames. 

May I ask you to help me, Please? 
Thank you very much in advance. 
Best Regards 
Sara
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Re: [gmx-users] parameters in *.mdp files

[Justin Lemkul]

On 8/19/12 9:29 AM, Shima Arasteh wrote:



Thanks for your reply.
Yes, using a better thermostat doesn't mean I have a longer simulation. But, a 
better thermostat has more ab-initio terms, which I think the calculation of 
them might be time consuming. That's why I guess I will have a longer 
simulation ( the time which the computer spends to simulate a system for 
adjusted time such as 50 ns).



I have never seen an appreciable difference between the performance obtained 
with different thermostats.  The time taken for coupling algorithms is 
negligible compared to the vastly more expensive calculations done during an MD 
simulation.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters in *.mdp files

[Shima Arasteh]

Thanks for your reply.
Yes, using a better thermostat doesn't mean I have a longer simulation. But, a 
better thermostat has more ab-initio terms, which I think the calculation of 
them might be time consuming. That's why I guess I will have a longer 
simulation ( the time which the computer spends to simulate a system for 
adjusted time such as 50 ns).


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Sunday, August 19, 2012 5:19 PM
Subject: Re: [gmx-users] parameters in *.mdp files



On 8/19/12 7:39 AM, Shima Arasteh wrote:
> Hi all,
> 
> In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp ,
> npt.mdp or md.mdp are the same. Is it necessary to use the same temperature
> coupling parameters in .mdp files? Generally, which parameters are supposed
> to be the same in .mdp files of a simulation?
> 

The thermostat can change.  Generally, the Berendsen method is advisable for 
initial NVT equilibration because it allows systems to relax gently.  Starting 
with Nose-Hoover, for instance, can lead to rapid instabilities and a crash. 
Once equilibrated, a more rigorous method should be used.

Nearly all .mdp settings are identical for any phase of a simulation 
(equilibration or data collection).  Most of the settings are dictated by the 
force field you've chosen, and since that's not changing, neither should your 
.mdp settings.  The thermostat might be adjusted, as stated above, and 
restraints removed or applied, tau_t or tau_p may be adjusted as the system 
reaches equilibrium.  Outside of these settings, everything else is generally 
static.

> 
> If a more accurate thermostat is used in a simulation, would it increase the
> time of simulation? What kind of simulations worthwhile a more accurate
> thermostats?
> 

You should always use an accurate thermostat.  Using a "better" thermostat does 
not mean you have to run your simulation longer.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters in *.mdp files

[Shima Arasteh]

Thanks for your reply.
Yes, using a better thermostat doesn't mean I have a longer simulation. But, a 
better thermostat has more ab-initio terms, which I think the calculation of 
them might be consuming. That's why I guess I will have a longer simulation ( 
the time which the computer spends simulate a system for adjusted time such as 
50 ns).


 
Sincerely,
Shima


- Original Message -
From: Justin Lemkul 
To: Shima Arasteh ; Discussion list for GROMACS 
users 
Cc: 
Sent: Sunday, August 19, 2012 5:19 PM
Subject: Re: [gmx-users] parameters in *.mdp files



On 8/19/12 7:39 AM, Shima Arasteh wrote:
> Hi all,
> 
> In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp ,
> npt.mdp or md.mdp are the same. Is it necessary to use the same temperature
> coupling parameters in .mdp files? Generally, which parameters are supposed
> to be the same in .mdp files of a simulation?
> 

The thermostat can change.  Generally, the Berendsen method is advisable for 
initial NVT equilibration because it allows systems to relax gently.  Starting 
with Nose-Hoover, for instance, can lead to rapid instabilities and a crash. 
Once equilibrated, a more rigorous method should be used.

Nearly all .mdp settings are identical for any phase of a simulation 
(equilibration or data collection).  Most of the settings are dictated by the 
force field you've chosen, and since that's not changing, neither should your 
.mdp settings.  The thermostat might be adjusted, as stated above, and 
restraints removed or applied, tau_t or tau_p may be adjusted as the system 
reaches equilibrium.  Outside of these settings, everything else is generally 
static.

> 
> If a more accurate thermostat is used in a simulation, would it increase the
> time of simulation? What kind of simulations worthwhile a more accurate
> thermostats?
> 

You should always use an accurate thermostat.  Using a "better" thermostat does 
not mean you have to run your simulation longer.

-Justin

-- 

Justin A. Lemkul, Ph.D.
Research Scientist
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
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http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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Re: [gmx-users] parameters in *.mdp files

[Justin Lemkul]

On 8/19/12 7:39 AM, Shima Arasteh wrote:

Hi all,

In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp ,
npt.mdp or md.mdp are the same. Is it necessary to use the same temperature
coupling parameters in .mdp files? Generally, which parameters are supposed
to be the same in .mdp files of a simulation?



The thermostat can change.  Generally, the Berendsen method is advisable for 
initial NVT equilibration because it allows systems to relax gently.  Starting 
with Nose-Hoover, for instance, can lead to rapid instabilities and a crash. 
Once equilibrated, a more rigorous method should be used.


Nearly all .mdp settings are identical for any phase of a simulation 
(equilibration or data collection).  Most of the settings are dictated by the 
force field you've chosen, and since that's not changing, neither should your 
.mdp settings.  The thermostat might be adjusted, as stated above, and 
restraints removed or applied, tau_t or tau_p may be adjusted as the system 
reaches equilibrium.  Outside of these settings, everything else is generally 
static.




If a more accurate thermostat is used in a simulation, would it increase the
time of simulation? What kind of simulations worthwhile a more accurate
thermostats?



You should always use an accurate thermostat.  Using a "better" thermostat does 
not mean you have to run your simulation longer.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters in *.mdp files

[Shima Arasteh]

Hi all,

In some simulations that I've studied, the "tcoupl"s chosen in nvt.mdp , 
npt.mdp or md.mdp are the same. Is it necessary to use the same temperature 
coupling parameters in .mdp files? Generally, which parameters are supposed to 
be the same in .mdp files of a simulation? 


If a more accurate thermostat is used in a simulation, would it increase the 
time of simulation? What kind of simulations worthwhile a more accurate 
thermostats?

I'm looking forward to get your replies. Thanks in advance.




Sincerely,
Shima 
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RE: [gmx-users] Parameters for bonded interactions

[Sebastien Cote]

Thanks Mark! This is exactly what I need. 


> Date: Wed, 15 Aug 2012 22:18:10 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Parameters for bonded interactions
>
> On 15/08/2012 8:44 PM, Sebastien Cote wrote:
> > After checking the post-processed topology, it does not contain the 
> > information that I need. I would like to know the torsion angle parameters 
> > of each torsion angle, and then compare with the ffbonded file to see the 
> > corresponding four-atom groups ' X X X X '.
> >
> > Is there a way to convert the .tpr file to 'human readable'?
>
> Sorry, meant to say that last email. gmxdump is all that is available.
> You'll have to work backwards from the atom numbers (starting counting
> from zero!) to get the interaction number to look up the interaction
> parameters from their list.
>
> Mark
>
> >
> > Thanks again,
> >
> > Sebastien
> >
> > --------
> >> Date: Wed, 15 Aug 2012 11:48:00 +1000
> >> From: mark.abra...@anu.edu.au
> >> To: gmx-users@gromacs.org
> >> Subject: Re: [gmx-users] Parameters for bonded interactions
> >>
> >> On 15/08/2012 9:46 AM, Sebastien Cote wrote:
> >>> Dear Gromacs users,
> >>>
> >>> In the topology file of the protein, we see every two atoms that share a 
> >>> bond, three atoms that share a bond angle, and four atoms that share a 
> >>> torsion angle. However, the parameters (equilibrium value, energy 
> >>> constant, phase) are not explicitly shown as Gromacs fetch them in the 
> >>> ffbonded table. My question: Is there a simple way to see (without having 
> >>> to look at the code) which parameters are associated to which bond 
> >>> length, bond angle and torsion angle?
> >>>
> >>> More specifically, I would like to know which torsion angle parameters is 
> >>> specifically associated to each torsion angle. In the ffbonded table, 
> >>> there is sometimes different groups of four atoms that can be associated 
> >>> to the same torsion angle as there is the 'X' atom which can be any atom.
> >> grompp -pp writes out a post-processed topology, which may be what you 
> >> need.
> >>
> >> Otherwise you can inspect the contents of the .tpr file to see which
> >> interaction gets which parameters. That is not easy for a large system,
> >> but is definitive.
> >>
> >> Mark
> >> --
> >> gmx-users mailing list gmx-users@gromacs.org
> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> * Only plain text messages are allowed!
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Re: [gmx-users] Parameters for bonded interactions

[Mark Abraham]

On 15/08/2012 8:44 PM, Sebastien Cote wrote:

After checking the post-processed topology, it does not contain the information 
that I need. I would like to know the torsion angle parameters of each torsion 
angle, and then compare with the ffbonded file to see the corresponding 
four-atom groups ' X X X X '.

Is there a way to convert the .tpr file to 'human readable'?


Sorry, meant to say that last email. gmxdump is all that is available. 
You'll have to work backwards from the atom numbers (starting counting 
from zero!) to get the interaction number to look up the interaction 
parameters from their list.


Mark



Thanks again,

Sebastien



Date: Wed, 15 Aug 2012 11:48:00 +1000
From: mark.abra...@anu.edu.au
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] Parameters for bonded interactions

On 15/08/2012 9:46 AM, Sebastien Cote wrote:

Dear Gromacs users,

In the topology file of the protein, we see every two atoms that share a bond, 
three atoms that share a bond angle, and four atoms that share a torsion angle. 
However, the parameters (equilibrium value, energy constant, phase) are not 
explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is 
there a simple way to see (without having to look at the code) which parameters 
are associated to which bond length, bond angle and torsion angle?

More specifically, I would like to know which torsion angle parameters is 
specifically associated to each torsion angle. In the ffbonded table, there is 
sometimes different groups of four atoms that can be associated to the same 
torsion angle as there is the 'X' atom which can be any atom.

grompp -pp writes out a post-processed topology, which may be what you need.

Otherwise you can inspect the contents of the .tpr file to see which
interaction gets which parameters. That is not easy for a large system,
but is definitive.

Mark
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RE: [gmx-users] Parameters for bonded interactions

[Sebastien Cote]

After checking the post-processed topology, it does not contain the information 
that I need. I would like to know the torsion angle parameters of each torsion 
angle, and then compare with the ffbonded file to see the corresponding 
four-atom groups ' X X X X '.

Is there a way to convert the .tpr file to 'human readable'?

Thanks again,

Sebastien  


> Date: Wed, 15 Aug 2012 11:48:00 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Parameters for bonded interactions
>
> On 15/08/2012 9:46 AM, Sebastien Cote wrote:
> > Dear Gromacs users,
> >
> > In the topology file of the protein, we see every two atoms that share a 
> > bond, three atoms that share a bond angle, and four atoms that share a 
> > torsion angle. However, the parameters (equilibrium value, energy constant, 
> > phase) are not explicitly shown as Gromacs fetch them in the ffbonded 
> > table. My question: Is there a simple way to see (without having to look at 
> > the code) which parameters are associated to which bond length, bond angle 
> > and torsion angle?
> >
> > More specifically, I would like to know which torsion angle parameters is 
> > specifically associated to each torsion angle. In the ffbonded table, there 
> > is sometimes different groups of four atoms that can be associated to the 
> > same torsion angle as there is the 'X' atom which can be any atom.
>
> grompp -pp writes out a post-processed topology, which may be what you need.
>
> Otherwise you can inspect the contents of the .tpr file to see which
> interaction gets which parameters. That is not easy for a large system,
> but is definitive.
>
> Mark
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] Parameters for bonded interactions

[Sebastien Cote]

Thanks a lot Mark!


> Date: Wed, 15 Aug 2012 11:48:00 +1000
> From: mark.abra...@anu.edu.au
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Parameters for bonded interactions
>
> On 15/08/2012 9:46 AM, Sebastien Cote wrote:
> > Dear Gromacs users,
> >
> > In the topology file of the protein, we see every two atoms that share a 
> > bond, three atoms that share a bond angle, and four atoms that share a 
> > torsion angle. However, the parameters (equilibrium value, energy constant, 
> > phase) are not explicitly shown as Gromacs fetch them in the ffbonded 
> > table. My question: Is there a simple way to see (without having to look at 
> > the code) which parameters are associated to which bond length, bond angle 
> > and torsion angle?
> >
> > More specifically, I would like to know which torsion angle parameters is 
> > specifically associated to each torsion angle. In the ffbonded table, there 
> > is sometimes different groups of four atoms that can be associated to the 
> > same torsion angle as there is the 'X' atom which can be any atom.
>
> grompp -pp writes out a post-processed topology, which may be what you need.
>
> Otherwise you can inspect the contents of the .tpr file to see which
> interaction gets which parameters. That is not easy for a large system,
> but is definitive.
>
> Mark
> --
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Re: [gmx-users] Parameters for bonded interactions

[Mark Abraham]

On 15/08/2012 9:46 AM, Sebastien Cote wrote:

Dear Gromacs users,

In the topology file of the protein, we see every two atoms that share a bond, 
three atoms that share a bond angle, and four atoms that share a torsion angle. 
However, the parameters (equilibrium value, energy constant, phase) are not 
explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is 
there a simple way to see (without having to look at the code) which parameters 
are associated to which bond length, bond angle and torsion angle?

More specifically, I would like to know which torsion angle parameters is 
specifically associated to each torsion angle. In the ffbonded table, there is 
sometimes different groups of four atoms that can be associated to the same 
torsion angle as there is the 'X' atom which can be any atom.


grompp -pp writes out a post-processed topology, which may be what you need.

Otherwise you can inspect the contents of the .tpr file to see which 
interaction gets which parameters. That is not easy for a large system, 
but is definitive.


Mark
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[gmx-users] Parameters for bonded interactions

[Sebastien Cote]

Dear Gromacs users,

In the topology file of the protein, we see every two atoms that share a bond, 
three atoms that share a bond angle, and four atoms that share a torsion angle. 
However, the parameters (equilibrium value, energy constant, phase) are not 
explicitly shown as Gromacs fetch them in the ffbonded table. My question: Is 
there a simple way to see (without having to look at the code) which parameters 
are associated to which bond length, bond angle and torsion angle?

More specifically, I would like to know which torsion angle parameters is 
specifically associated to each torsion angle. In the ffbonded table, there is 
sometimes different groups of four atoms that can be associated to the same 
torsion angle as there is the 'X' atom which can be any atom.

Thanks for your help,

Sebastien --
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Re: [gmx-users] parameters for bond types for GROMOS force field.

[Mark Abraham]

On 11/06/2012 6:12 PM, James Starlight wrote:

Justin


1) So if I understood correctly I can make parametrisation of my 
uncommon group by the atb for instance. Than I can change itp file to 
rtp form and integrate this new residue to the existing ff. Finally 
when I will run pdb2gmx on the protein with the same group (even with 
different atom order) I obtain proper topology.top file. Doest it 
correct ?


The "change" to which you refer will be non-trivial because of the 
covalent bond. Charge distribution and atom types will change.




2) I've defined bond between both of my atoms as the  gb_15 and define 
this atoms as the C in the topology.top. Than I've run minimisation 
and short 3ns MD_run. Unfortunatelly this atoms was in the sp3 form 
and were not in the planar form :(  What else should I do ? Could some 
operations with the angle term in topology.top help me? I've modified  
612   613   614 2 as thega_27   but it also could not help me.


It is possible to hack something that will work, but the transferability 
of charges from an isolated form to a form covalently bound to a peptide 
is (at best) doubtful. If your atomic arrangement is changing, the 
presence of single vs double bonds must be changing, and that should 
basically guarantee non-transferability.


The most correct form of a solution is to parameterise the modified form 
of the residue along the same lines as the original force field 
parameterization. That may or may not be feasible for you. It's hard to 
be more specific without knowing exactly what modified residue you are 
seeking to create.


Mark





James

2012/6/10 Justin A. Lemkul mailto:jalem...@vt.edu>>



On 6/10/12 8:03 AM, James Starlight wrote:

Justin,

thanks again for help.

Finally is there any generall solution to parametrise
hetero-groups covalently
bonded with the protein ? Many proteins consist of such groups
e.g chromophore
in GFP, retinall in rhodopsin as well as some prostetic groups
in the enzymes.


Parameterization schemes differ across force fields.  It's never
easy.


I've tried to make something like you've told me via inclusion of
pre-parametrised residues in the existing gromacs ff but
forced with some
problems due to the atom order in new ITP and gro files
provided by ATb or
PRODRG are different from initial pdb file so pdb2gmx on the
whole protein where
het-group in the old order would not work properly :(


The output .itp files of ATB or PRODRG are not what you should be
using.  You can't #include a covalently attached residue and
expect the resulting dynamics to be relevant; it's not like a ligand.

What you need to do in those cases is create an .rtp entry (and
any other incidental bonded and nonbonded additions, as stated
before) that specifies whatever parameters you believe to be
reliable.  At that point, when the .rtp file is read, the atom
order is irrelevant - if pdb2gmx finds the atoms it needs, it
builds the topology.


-Justin

-- 



Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for bond types for GROMOS force field.

[James Starlight]

Justin


1) So if I understood correctly I can make parametrisation of my uncommon
group by the atb for instance. Than I can change itp file to rtp form and
integrate this new residue to the existing ff. Finally when I will run
pdb2gmx on the protein with the same group (even with different atom order)
I obtain proper topology.top file. Doest it correct ?


2) I've defined bond between both of my atoms as the  gb_15 and define this
atoms as the C in the topology.top. Than I've run minimisation and short
3ns MD_run. Unfortunatelly this atoms was in the sp3 form and were not in
the planar form :(  What else should I do ? Could some operations with the
angle term in topology.top help me? I've modified  612   613   614 2 as
thega_27   but it also could not help me.



James

2012/6/10 Justin A. Lemkul 

>
>
> On 6/10/12 8:03 AM, James Starlight wrote:
>
>> Justin,
>>
>> thanks again for help.
>>
>> Finally is there any generall solution to parametrise hetero-groups
>> covalently
>> bonded with the protein ? Many proteins consist of such groups e.g
>> chromophore
>> in GFP, retinall in rhodopsin as well as some prostetic groups in the
>> enzymes.
>>
>>
> Parameterization schemes differ across force fields.  It's never easy.
>
>
>  I've tried to make something like you've told me via inclusion of
>> pre-parametrised residues in the existing gromacs ff but forced with some
>> problems due to the atom order in new ITP and gro files provided by ATb or
>> PRODRG are different from initial pdb file so pdb2gmx on the whole
>> protein where
>> het-group in the old order would not work properly :(
>>
>>
> The output .itp files of ATB or PRODRG are not what you should be using.
>  You can't #include a covalently attached residue and expect the resulting
> dynamics to be relevant; it's not like a ligand.
>
> What you need to do in those cases is create an .rtp entry (and any other
> incidental bonded and nonbonded additions, as stated before) that specifies
> whatever parameters you believe to be reliable.  At that point, when the
> .rtp file is read, the atom order is irrelevant - if pdb2gmx finds the
> atoms it needs, it builds the topology.
>
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] parameters for bond types for GROMOS force field.

[Justin A. Lemkul]

On 6/10/12 8:03 AM, James Starlight wrote:

Justin,

thanks again for help.

Finally is there any generall solution to parametrise hetero-groups covalently
bonded with the protein ? Many proteins consist of such groups e.g chromophore
in GFP, retinall in rhodopsin as well as some prostetic groups in the enzymes.



Parameterization schemes differ across force fields.  It's never easy.


I've tried to make something like you've told me via inclusion of
pre-parametrised residues in the existing gromacs ff but forced with some
problems due to the atom order in new ITP and gro files provided by ATb or
PRODRG are different from initial pdb file so pdb2gmx on the whole protein where
het-group in the old order would not work properly :(



The output .itp files of ATB or PRODRG are not what you should be using.  You 
can't #include a covalently attached residue and expect the resulting dynamics 
to be relevant; it's not like a ligand.


What you need to do in those cases is create an .rtp entry (and any other 
incidental bonded and nonbonded additions, as stated before) that specifies 
whatever parameters you believe to be reliable.  At that point, when the .rtp 
file is read, the atom order is irrelevant - if pdb2gmx finds the atoms it 
needs, it builds the topology.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for bond types for GROMOS force field.

[James Starlight]

Justin,

thanks again for help.

Finally is there any generall solution to parametrise hetero-groups
covalently bonded with the protein ? Many proteins consist of such groups
e.g chromophore in GFP, retinall in rhodopsin as well as some prostetic
groups in the enzymes.

I've tried to make something like you've told me via inclusion of
pre-parametrised residues in the existing gromacs ff but forced with some
problems due to the atom order in new ITP and gro files provided by ATb or
PRODRG are different from initial pdb file so pdb2gmx on the whole protein
where het-group in the old order would not work properly :(

James

2012/6/10 Justin A. Lemkul 

>
>
> On 6/10/12 3:06 AM, James Starlight wrote:
>
>> Justin
>>
>> I have one extra question about parametrisation of the bond type
>>
>> Initially I had -c-c- bond so both atoms were in the sp3 hybridization.
>> I've
>> changed bond type between that atoms to the gb_16 ( from phe ring) to
>> define
>> them as the >c=c< but during the simulation I've noticed that the bond
>> between
>> that atoms is not planar ( sp2 form) and still is in the sp3. What
>> addition
>> changees should I do in my topology to change the planarity of new bond ?
>>
>>
>>
> Defining appropriate atom types will be necessary here, as well.  For a
> single bond, the atom types would be -CH2-CH2- while a double bond will
> necessarily be -CH=CH-
>
> Also note that with a united atom representation, it's very hard to make
> such assertions about hybridization state.  There are no hydrogens, so the
> geometry of these central carbons is not easily defined.
>
>
>  Should I make some changes ia angles term as well?
>>
>> E.g I've found
>>
>>   612   613   614 2ga_13  ;
>>
>> where 612 and 613 are the atoms wich I would like to present as the
>> rigid. I've
>> change to the ga_27 ( 120) but during simulation the bond was still in
>> sp3. What
>> I've done wrong ?
>>
>>
> As there are no parameters for linear C=C bonds in the Gromos force
> fields, you may have to do some parameterization yourself, particularly for
> appropriate dihedrals.  One option is to look at how these bonds are
> treated in lipid force fields like the Berger parameter set, distributed by
> Peter Tieleman's group. There are double bonds defined for lipids like POPC.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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] parameters for bond types for GROMOS force field.

[Justin A. Lemkul]

On 6/10/12 3:06 AM, James Starlight wrote:

Justin

I have one extra question about parametrisation of the bond type

Initially I had -c-c- bond so both atoms were in the sp3 hybridization. I've
changed bond type between that atoms to the gb_16 ( from phe ring) to define
them as the >c=c< but during the simulation I've noticed that the bond between
that atoms is not planar ( sp2 form) and still is in the sp3. What addition
changees should I do in my topology to change the planarity of new bond ?




Defining appropriate atom types will be necessary here, as well.  For a single 
bond, the atom types would be -CH2-CH2- while a double bond will necessarily be 
-CH=CH-


Also note that with a united atom representation, it's very hard to make such 
assertions about hybridization state.  There are no hydrogens, so the geometry 
of these central carbons is not easily defined.



Should I make some changes ia angles term as well?

E.g I've found

   612   613   614 2ga_13  ;

where 612 and 613 are the atoms wich I would like to present as the rigid. I've
change to the ga_27 ( 120) but during simulation the bond was still in sp3. What
I've done wrong ?



As there are no parameters for linear C=C bonds in the Gromos force fields, you 
may have to do some parameterization yourself, particularly for appropriate 
dihedrals.  One option is to look at how these bonds are treated in lipid force 
fields like the Berger parameter set, distributed by Peter Tieleman's group. 
There are double bonds defined for lipids like POPC.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for bond types for GROMOS force field.

[James Starlight]

Justin

I have one extra question about parametrisation of the bond type

Initially I had -c-c- bond so both atoms were in the sp3 hybridization.
I've changed bond type between that atoms to the gb_16 ( from phe ring) to
define them as the >c=c< but during the simulation I've noticed that the
bond between that atoms is not planar ( sp2 form) and still is in the sp3.
What addition changees should I do in my topology to change the planarity
of new bond ?


Should I make some changes ia angles term as well?

E.g I've found

  612   613   614 2ga_13  ;

where 612 and 613 are the atoms wich I would like to present as the rigid.
I've change to the ga_27 ( 120) but during simulation the bond was still in
sp3. What I've done wrong ?

James

2012/6/8 James Starlight 

> Justin,
>
>
>
> thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C)
> for parametrisation in my task.
>
>
>
> James
>
> 2012/6/8 Justin A. Lemkul 
>
>>
>>
>> On 6/8/12 2:01 PM, James Starlight wrote:
>>
>>> Justin,
>>>
>>> Does the gb_10 suitable for both bonds that I want to parametrise ?
>>>
>>> As I've told previously I need to parametrise two different bonds
>>>
>>> 1) is the >C=C< bond wich are not in the ring. This is just double bound
>>> in
>>> linnear sequence -C=C-.
>>>
>>> 2) is the >C=N- double bond where both atoms in the 5-m ring system
>>>
>>>
>> This is a better description.  The last message suggested everything was
>> in a 5-membered ring.  Had that been the case, my suggestion would have
>> been right (see, for instance, a HIS side chain - gb_10 is used for both
>> C=C and C=N in that case).
>>
>> There are no linear C=C bonds in Gromos force fields by default, as such
>> groups are not in proteins.  The closest you can likely come is to take a
>> C=C bond from the PHE ring.  Bond lengths are simple, and are usually
>> derived from spectroscopic information.  If using constraints on all bonds,
>> the force constant is irrelevant since the bond is rigid.  If not using
>> constraints, then you'll have to find or derive suitable parameters
>> yourself.  Welcome to the inconvenient world of parameterization :)
>>
>> -Justin
>>
>>  Thanks again,
>>>
>>> James
>>>
>>>
>>>
>>> 2012/6/8 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>>
>>>
>>>
>>>
>>>On 6/8/12 1:22 PM, James Starlight wrote:
>>>
>>>I've found that information in ffbonded.itp but I'm not sure
>>> about exactly
>>>meaning of some types.
>>>
>>>
>>>E.g I'm looking for bond type for simple double bond between C=C
>>> as well
>>>as C=N
>>>( here both atoms in 5-m ring) atoms pairs. Should I use for the
>>> first one
>>>#define gb_15   0.1390  8.6600e+06
>>>; CH2  -  C, CR1 (6-ring)   800
>>>
>>>   and for the second one ;
>>>
>>>#define gb_11   0.1340  1.0500e+07
>>>; C  -  N, NZ, NE   900
>>>?
>>>
>>>
>>>Neither.  gb_10 sounds exactly like what you need:
>>>
>>>#define gb_10   0.1330  1.1800e+07
>>>; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000
>>>
>>>-Justin
>>>
>>>--
>>>==**__==
>>>
>>>
>>>Justin A. Lemkul, Ph.D.
>>>Research Scientist
>>>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 >> gmx-users@gromacs.org>
>>>
>>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>>
>>>
>>> 
>>> >
>>>Please search the archive at
>>>
>>> http://www.gromacs.org/__**Support/Mailing_Lists/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/__**Support/Mailing_Lists
>>>
>>> 
>>> >
>>>
>>>
>>>
>> --
>> ==**==
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.bi

Re: [gmx-users] parameters for bond types for GROMOS force field.

[James Starlight]

Justin,



thanks alot. I'll try to use gb_10 ( for C=N) as well as gb_16 ( for C=C)
for parametrisation in my task.


James

2012/6/8 Justin A. Lemkul 

>
>
> On 6/8/12 2:01 PM, James Starlight wrote:
>
>> Justin,
>>
>> Does the gb_10 suitable for both bonds that I want to parametrise ?
>>
>> As I've told previously I need to parametrise two different bonds
>>
>> 1) is the >C=C< bond wich are not in the ring. This is just double bound
>> in
>> linnear sequence -C=C-.
>>
>> 2) is the >C=N- double bond where both atoms in the 5-m ring system
>>
>>
> This is a better description.  The last message suggested everything was
> in a 5-membered ring.  Had that been the case, my suggestion would have
> been right (see, for instance, a HIS side chain - gb_10 is used for both
> C=C and C=N in that case).
>
> There are no linear C=C bonds in Gromos force fields by default, as such
> groups are not in proteins.  The closest you can likely come is to take a
> C=C bond from the PHE ring.  Bond lengths are simple, and are usually
> derived from spectroscopic information.  If using constraints on all bonds,
> the force constant is irrelevant since the bond is rigid.  If not using
> constraints, then you'll have to find or derive suitable parameters
> yourself.  Welcome to the inconvenient world of parameterization :)
>
> -Justin
>
>  Thanks again,
>>
>> James
>>
>>
>>
>> 2012/6/8 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>On 6/8/12 1:22 PM, James Starlight wrote:
>>
>>I've found that information in ffbonded.itp but I'm not sure about
>> exactly
>>meaning of some types.
>>
>>
>>E.g I'm looking for bond type for simple double bond between C=C
>> as well
>>as C=N
>>( here both atoms in 5-m ring) atoms pairs. Should I use for the
>> first one
>>#define gb_15   0.1390  8.6600e+06
>>; CH2  -  C, CR1 (6-ring)   800
>>
>>   and for the second one ;
>>
>>#define gb_11   0.1340  1.0500e+07
>>; C  -  N, NZ, NE   900
>>?
>>
>>
>>Neither.  gb_10 sounds exactly like what you need:
>>
>>#define gb_10   0.1330  1.1800e+07
>>; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000
>>
>>-Justin
>>
>>--
>>==**__==
>>
>>
>>Justin A. Lemkul, Ph.D.
>>Research Scientist
>>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 > gmx-users@gromacs.org>
>>
>> http://lists.gromacs.org/__**mailman/listinfo/gmx-users
>>
>>
>> 
>> >
>>Please search the archive at
>>
>> http://www.gromacs.org/__**Support/Mailing_Lists/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/__**Support/Mailing_Lists
>>
>> 
>> >
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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Re: [gmx-users] parameters for bond types for GROMOS force field.

[Justin A. Lemkul]

On 6/8/12 2:01 PM, James Starlight wrote:

Justin,

Does the gb_10 suitable for both bonds that I want to parametrise ?

As I've told previously I need to parametrise two different bonds

1) is the >C=C< bond wich are not in the ring. This is just double bound in
linnear sequence -C=C-.

2) is the >C=N- double bond where both atoms in the 5-m ring system



This is a better description.  The last message suggested everything was in a 
5-membered ring.  Had that been the case, my suggestion would have been right 
(see, for instance, a HIS side chain - gb_10 is used for both C=C and C=N in 
that case).


There are no linear C=C bonds in Gromos force fields by default, as such groups 
are not in proteins.  The closest you can likely come is to take a C=C bond from 
the PHE ring.  Bond lengths are simple, and are usually derived from 
spectroscopic information.  If using constraints on all bonds, the force 
constant is irrelevant since the bond is rigid.  If not using constraints, then 
you'll have to find or derive suitable parameters yourself.  Welcome to the 
inconvenient world of parameterization :)


-Justin


Thanks again,

James



2012/6/8 Justin A. Lemkul mailto:jalem...@vt.edu>>



On 6/8/12 1:22 PM, James Starlight wrote:

I've found that information in ffbonded.itp but I'm not sure about 
exactly
meaning of some types.


E.g I'm looking for bond type for simple double bond between C=C as well
as C=N
( here both atoms in 5-m ring) atoms pairs. Should I use for the first 
one
#define gb_15   0.1390  8.6600e+06
; CH2  -  C, CR1 (6-ring)   800

   and for the second one ;

#define gb_11   0.1340  1.0500e+07
; C  -  N, NZ, NE   900
?


Neither.  gb_10 sounds exactly like what you need:

#define gb_10   0.1330  1.1800e+07
; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000

-Justin

--
==__==

Justin A. Lemkul, Ph.D.
Research Scientist
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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--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for bond types for GROMOS force field.

[James Starlight]

Justin,

Does the gb_10 suitable for both bonds that I want to parametrise ?

As I've told previously I need to parametrise two different bonds

1) is the >C=C< bond wich are not in the ring. This is just double bound in
linnear sequence -C=C-.

2) is the >C=N- double bond where both atoms in the 5-m ring system

Thanks again,

James



2012/6/8 Justin A. Lemkul 

>
>
> On 6/8/12 1:22 PM, James Starlight wrote:
>
>> I've found that information in ffbonded.itp but I'm not sure about exactly
>> meaning of some types.
>>
>>
>> E.g I'm looking for bond type for simple double bond between C=C as well
>> as C=N
>> ( here both atoms in 5-m ring) atoms pairs. Should I use for the first one
>> #define gb_15   0.1390  8.6600e+06
>> ; CH2  -  C, CR1 (6-ring)   800
>>
>>   and for the second one ;
>>
>> #define gb_11   0.1340  1.0500e+07
>> ; C  -  N, NZ, NE   900
>> ?
>>
>>
> Neither.  gb_10 sounds exactly like what you need:
>
> #define gb_10   0.1330  1.1800e+07
> ; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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 listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
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> interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
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Re: [gmx-users] parameters for bond types for GROMOS force field.

[Justin A. Lemkul]

On 6/8/12 1:22 PM, James Starlight wrote:

I've found that information in ffbonded.itp but I'm not sure about exactly
meaning of some types.


E.g I'm looking for bond type for simple double bond between C=C as well as C=N
( here both atoms in 5-m ring) atoms pairs. Should I use for the first one
#define gb_15   0.1390  8.6600e+06
; CH2  -  C, CR1 (6-ring)   800

   and for the second one ;

#define gb_11   0.1340  1.0500e+07
; C  -  N, NZ, NE   900
?



Neither.  gb_10 sounds exactly like what you need:

#define gb_10   0.1330  1.1800e+07
; C, CR1  -  N, NR, CR1, C (peptide, 5-ring)   1000

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
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] parameters for bond types for GROMOS force field.

[James Starlight]

I've found that information in ffbonded.itp but I'm not sure about exactly
meaning of some types.


E.g I'm looking for bond type for simple double bond between C=C as well as
C=N ( here both atoms in 5-m ring) atoms pairs. Should I use for the first
one
#define gb_15   0.1390  8.6600e+06
; CH2  -  C, CR1 (6-ring)   800

  and for the second one ;

#define gb_11   0.1340  1.0500e+07
; C  -  N, NZ, NE   900
?

Thanks for help

James

2012/6/8 Mark Abraham 

> On 9/06/2012 12:00 AM, James Starlight wrote:
>
>> Dear Gromacs Users!
>>
>>
>> I'm looking for description of the parameters of bonds terms ( termed as
>> the gb_# in the topology.top file) . Could you tell me where I could find
>> such descriptions for all possible bond types ?
>>
>
> See manual for literature references for the force field components.
>
> Mark
> --
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Re: [gmx-users] parameters for bond types for GROMOS force field.

[Mark Abraham]

On 9/06/2012 12:00 AM, James Starlight wrote:

Dear Gromacs Users!


I'm looking for description of the parameters of bonds terms ( termed 
as the gb_# in the topology.top file) . Could you tell me where I 
could find such descriptions for all possible bond types ?


See manual for literature references for the force field components.

Mark
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[gmx-users] parameters for bond types for GROMOS force field.

[James Starlight]

Dear Gromacs Users!


I'm looking for description of the parameters of bonds terms ( termed as
the gb_# in the topology.top file) . Could you tell me where I could find
such descriptions for all possible bond types ?



thanks,

James
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[gmx-users] parameters of a residue

[Shima Arasteh]

Dear gmx users,
Corresponding to your suggestions, I get the parameters for new defined 
residues from SwissParam. The parameters are not accurate completely. May I 
face any problem when getting the PMF? and specially for publishing a paper for 
this reason that the parameters are not accurate as well as what is supposed to 
be.

Thanks in advance,

Sincerely,
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[gmx-users] parameters and restrains for Fe3+

[Carla]

Hi,
I need to introduce new atomtypes/parameters and restrains in Gromacs for
Fe3+. Could you please inform me on how can I do it?
Thanks.

Cheers,
Carla 

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Re: [gmx-users] parameters of em.mdp

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear Justin,

Thanks for your reply. You said "You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called 
"Tutorial 5: Protein-Ligand Complex".

_*a part of your em.mdp*_
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
_*a part of your md.mdp*_
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4

Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) 
for energy minimization?




In my experience, the outcome of EM is not particularly sensitive to those types 
of changes for very robust systems, especially in single precision.  The energy 
values and maximum forces achieved don't change appreciably in most cases.


Regarding nstlist, for EM it should be set to 1.

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] parameters of em.mdp

[ahmet yıldırım]

Dear Justin,

Thanks for your reply. You said "You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called
"Tutorial 5: Protein-Ligand Complex".
*a part of your em.mdp*
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
*a part of your md.mdp*
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4

Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw) for
energy minimization?

Thanks in advance

23 Mart 2012 19:31 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> I am using the Reaction-Field method for electrostatics interactions. I
>> used the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp,
>> npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set
>> nstlist=rlist=rcoulomb=rvdw=1.**0 for energy minimization, would not it
>> be better? What is your suggestions?
>>
>>
> Why do you think making such changes to the cutoffs would be better?
>  These settings, for the most part, are a fixed part of the force field
> you're using. Unless you have proof (either by your own demonstration or
> one that is published) that making such changes result in better results,
> you should avoid ad hoc changes.
>
>  ; Neighbor Searching Parameters
>> nstlist = 5 ns-type = Grid   pbc
>>= xyz   rlist   = 0.9 ;
>> Electrostatics
>> coulombtype = Reaction-Field rcoulomb= 1.4
>>   epsilon_rf  = 54   ; VdW
>> vdw-type= Cut-off rvdw= 1.4
>> *
>> Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp,
>> npt.mdp and md.mdp) the reference temperature for coupling. I analysed the
>> temperature after production run. I get "Temperature=312.646" (g_energy -f
>> md.edr -o temperature.xvg). that is, The temperature has increased
>> (approximately 12 K) during the simulation. What could be the reason for
>> the increase in temperature? I had setted to 200 K the reference
>> temperature for coupling in pr.mdp. it can cause?
>>
>>
> This outcome is precisely what you would expect, simply because you're
> using the reaction field method and it introduces cutoff artifacts.
>  Interestingly, this same outcome (an increase of exactly 12K) has been
> reported before:
>
> http://lists.gromacs.org/**pipermail/gmx-users/2009-**January/039113.html
>
> -Justin
>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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>



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Re: [gmx-users] parameters of em.mdp

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,

I am using the Reaction-Field method for electrostatics interactions. I 
used the following parameters for all input files (em.mdp, pr.mdp, 
nvt.mdp, npt.mdp, md.mdp). I just changed as an epsilon_rf=78 in md.mdp. 
If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would 
not it be better? What is your suggestions?




Why do you think making such changes to the cutoffs would be better?  These 
settings, for the most part, are a fixed part of the force field you're using. 
Unless you have proof (either by your own demonstration or one that is 
published) that making such changes result in better results, you should avoid 
ad hoc changes.



; Neighbor Searching Parameters
nstlist = 5 
ns-type = Grid   
pbc= xyz   
rlist   = 0.9 
; Electrostatics
coulombtype = Reaction-Field 
rcoulomb= 1.4 
epsilon_rf  = 54   
; VdW
vdw-type= Cut-off 
rvdw= 1.4   
*
Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, 
npt.mdp and md.mdp) the reference temperature for coupling. I analysed 
the temperature after production run. I get "Temperature=312.646" 
(g_energy -f md.edr -o temperature.xvg). that is, The temperature has 
increased (approximately 12 K) during the simulation. What could be the 
reason for the increase in temperature? I had setted to 200 K the 
reference temperature for coupling in pr.mdp. it can cause?




This outcome is precisely what you would expect, simply because you're using the 
reaction field method and it introduces cutoff artifacts.  Interestingly, this 
same outcome (an increase of exactly 12K) has been reported before:


http://lists.gromacs.org/pipermail/gmx-users/2009-January/039113.html

-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] parameters of em.mdp

[ahmet yıldırım]

Dear users,

I am using the Reaction-Field method for electrostatics interactions.
I used the
following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp,
md.mdp). I just changed as an epsilon_rf=78 in md.mdp. If I set
nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be
better? What is your suggestions?

; Neighbor Searching Parameters
nstlist = 5
ns-type = Grid
pbc= xyz
rlist   = 0.9
; Electrostatics
coulombtype = Reaction-Field
rcoulomb= 1.4
epsilon_rf  = 54
; VdW
vdw-type= Cut-off
rvdw= 1.4
*
Another question:* I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp
and md.mdp) the reference temperature for coupling. I analysed the
temperature after production run. I get "Temperature=312.646" (g_energy -f
md.edr -o temperature.xvg). that is, The temperature has increased
(approximately
12 K) during the simulation. What could be the reason for the increase in
temperature? I had setted to 200 K the reference temperature for coupling
in pr.mdp. it can cause?

My em.mdp file is as the following:
*em.mdp:*
title= Energy Minimization ; Title of run
cpp= /lib/cpp ; Preprocessor: Line tell the program
the standard locations where to find certain files
define  = -DFLEXIBLE  ; defines to pass to the
preprocessor

; Run Control
integrator= steep; steep integrator (steep = steepest
descent minimization)
nsteps= 2500; maximum number of steps to integrate

; Energy Minimization
emtol= 1000.0 ; [kJ/mol/nm] minimization is
converged when max force is < emtol
emstep  = 0.01   ; [nm] initial step-size

; Output Control
nstxout = 0 ; [steps] freq to write coordinates
to trajectory
nstvout = 0 ; [steps] freq to write velocities
to trajectory
nstfout = 0 ; [steps] freq to write forces to
trajectory
nstlog  = 1 ; [steps] freq to write energies to
log file
nstenergy= 1; [steps] freq to write energies to energy
file
energygrps= System; group(s) to write to energy file

; Neighbor Searching Parameters
nstlist = 5 ; [steps] freq to update
neighbor list
ns-type = Grid  ; method of updating neighbor
list
pbc= xyz; periodic boundary conditions
(yes/no)in all directions
rlist   = 0.9   ; [nm] cut-off distance for the
short-range neighbor list

; Electrostatics
coulombtype = Reaction-Field  ; Reaction-Field electrostatics
rcoulomb= 1.4 ; [nm] distance for Coulomb
cut-off
epsilon_rf  = 54  ; The relative dielectric
constant of the reaction field

; VdW
vdw-type= Cut-off   ; twin-range cut-off with rlist
where rvdw >= rlist
rvdw= 1.4   ; [nm] distance for LJ cut-off

; Bonds
constraints = none ; convert all bonds to constraints

-- 
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Re: [gmx-users] parameters for CH1 -- S -- CH2 ?

[Mark Abraham]

On 20/08/2011 1:57 AM, Yun Shi wrote:

Hi all,

I have a small molecule with a part like:

CH1 --- CH1 --- S --- CH2 --- CH1
 |
 CH1

I first tried PRODRG, and it turned out PRODRG assigned bond, angle, 
and dihedral parameters according what are already present in the 
gromos53a6.ff/ffbonded.itp file. Since this file does not contain 
information regarding this CH1 --- S --- CH2 pattern, PRODRG just 
assigned bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- 
CH2 pattern, and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if 
it was CH1 -- CH2 -- S -- CH2.


So I guess I have to do this manually. But as no corresponding 
parameters defined in ffbonded.itp file, should I derive these 
parameters via chemical intuition and try validate them in some way?


Or is there an easier alternative way to do this?


Parameterizing new species is not easy. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization. Be sure 
to check the literature for existing approaches - and particularly how 
the thioether parameters that do exist were derived.


Mark

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[gmx-users] parameters for CH1 -- S -- CH2 ?

[Yun Shi]

Hi all,

I have a small molecule with a part like:

CH1 --- CH1 --- S --- CH2 --- CH1
 |
 CH1

I first tried PRODRG, and it turned out PRODRG assigned bond, angle, and
dihedral parameters according what are already present in the
gromos53a6.ff/ffbonded.itp file. Since this file does not contain
information regarding this CH1 --- S --- CH2 pattern, PRODRG just assigned
bond (gb_31),angle (ga_4) as if my molecule has CH3 --- S --- CH2 pattern,
and dihedral parameters for CH1 -- CH1 -- S -- CH2 as if it was CH1 -- CH2
-- S -- CH2.

So I guess I have to do this manually. But as no corresponding parameters
defined in ffbonded.itp file, should I derive these parameters via chemical
intuition and try validate them in some way?

Or is there an easier alternative way to do this?

Thanks for any suggestion!

Yun
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[gmx-users] Parameters for DMPG and G53a6 force field

[Krzysztof Mlynarczyk]

Hello,
I need parameters for DMPG membrane (G53a6 force field). Does anybody know
where I could find a tested parameter set and pdb file? If not, I believe I
could construct my own from e.g. Kukol A, Lipid Models for United-Atom
Molecular Dynamics Simulations of Proteins, DOI: 10.1021/ct8003468 by
merging PG parameters from POPG and the rest of the molecule from DMPC.

Thank you,
Christopher
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[gmx-users] Parameters for selenium

[chris . neale]

I don't have the parameters. You could possibly fudge it by  
extrapolating out from SER->CYS->Se_CYS based scaled by  
electronegativities of O,S,Se. I'm not saying that this is rigorous,  
just that its possible to do. My main point here, though, is to ask if  
you *really* need to bother with this.


Thioredoxin ~ 100 amino acids. Sampling is a real problem in  
simulations, and I highly doubt that you're going to see a difference  
in CYS vs. Se_CYS in the context of a 100 aa protein on simulation  
timescales (I also doubt you'd see a difference for CYS vs. SER).  
Besides, wouldn't crystallographers be basically out of business if  
Se_CYS mucked up the structure as compared to CYS?


Chris.



Please

Someone know Gromos parameters for selenium.  WE need to simulate the
Thioredoxin and we need to simulate a cisteine with a selenium.

Thanks
regards

Luis Scott

--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de Matemática, Computação e Cognição
Universidade Federal do ABC
Grupo de Pesquisa em Biologia Computacional






--
Prof. Dr. Luis Paulo Scott
CMCC- Centro de Matemática, Computação e Cognição
Universidade Federal do ABC


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Re: [gmx-users] Parameters for AOT molecule/Too few parameters on line

[Justin A. Lemkul]

Lum Nforbi wrote:

Hello all,

I have built a parameter file for the AOT surfactant molecule and 
tried to minimize the energy of a mixture of several of this molecule 
and water molecules but I have the warnings at the bottom part of this 
mail. Gromacs basically goes through all the lines of parameters 
starting from [ bonds ] and says the parameters are too few. I am also 
using the charmm force field.


Here is the way I constructed the aot.itp parameter file. I am not 
sure this is correct. Excerpts of the parameter file are belowl.


- I drew the AOT molecule and did the bond and angle connections in the 
molecule.The atom names are provided by the ffcharmm27.atp file. All 


The .atp file contains atom types, not atom names.  Your [bonds], [angles], etc. 
 should be numbers, not atom types or names.  For instance, if atoms 1 and 2 
are bonded:


[ bonds ]
12(function type, etc)


values are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file.
- I am not sure how to build the dihedrals since the are X's in the [ 
dihedrals ] section of the ffcharmmbon.itp file.




As Mark indicated earlier, an X is simply a wildcard - it can correspond to any 
number of atom types.


My question is: Why does the program say I have few parameters while I 
just out together parameters from the charmm27 force field? Please, if I 
am doing something wrong, can someone let me know?

  [ bonds ]
; ijfuncb0kb
SLO2L10.1448451872.0


You're using either atom types or names in these sections, which is completely 
incorrect.  Please have a thorough read through Chapter 5 of the manual.





NOTE 1 [file aotwater.top, line 19]:
  System has non-zero total charge: -1.35e+01
 


I would also be *very* concerned about this line.  You have a negative charge of 
-13.5, indicating that whatever charges you've assigned to your small molecule 
have left a fractional charge on the system, which is clearly non-physical.


-Justin


processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:60  OTHER residues
There are: 0PROTEIN residues
There are: 0DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 1110 elements
Making dummy/rest group for Acceleration containing 1110 elements
Making dummy/rest group for Freeze containing 1110 elements
Making dummy/rest group for Energy Mon. containing 1110 elements
Making dummy/rest group for VCM containing 1110 elements
Number of degrees of freedom in T-Coupling group rest is 3192.00
Making dummy/rest group for User1 containing 1110 elements
Making dummy/rest group for User2 containing 1110 elements
Making dummy/rest group for XTC containing 1110 elements
Making dummy/rest group for Or. Res. Fit containing 1110 elements
Making dummy/rest group for QMMM containing 1110 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file aotwater_min.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 1 Mb of data
writing run input file...

There were 2 notes

There were 142 warnings

---
Program grompp, VERSION 4.0.5
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (142), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
---


I appreciate your answers.

Lum



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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] Parameters for AOT molecule/Too few parameters on line

[Lum Nforbi]

Hello all,

I have built a parameter file for the AOT surfactant molecule and tried
to minimize the energy of a mixture of several of this molecule and water
molecules but I have the warnings at the bottom part of this mail. Gromacs
basically goes through all the lines of parameters starting from [ bonds ]
and says the parameters are too few. I am also using the charmm force field.


Here is the way I constructed the aot.itp parameter file. I am not sure
this is correct. Excerpts of the parameter file are belowl.

- I drew the AOT molecule and did the bond and angle connections in the
molecule.The atom names are provided by the ffcharmm27.atp file. All values
are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file.
- I am not sure how to build the dihedrals since the are X's in the [
dihedrals ] section of the ffcharmmbon.itp file.

My question is: Why does the program say I have few parameters while I just
out together parameters from the charmm27 force field? Please, if I am doing
something wrong, can someone let me know?
  [ bonds ]
; ijfuncb0kb
SLO2L10.1448451872.0
SL  CTL11   0.1800  376560.0
CTL1HAL110.258571.2
[ angles ]
; ijkfuncth0cthub0cub
02L SL  O2L 5   109.471087.840.24529288.0
O2L SL  CTL15   98.0711.280.00.0
SL  CTL1HAL15   110.10288.6960.217918853.104
[ dihedrals ]
; ijklfuncphi0cpmult
HAL1CTL1SLO2L90.000.03
CTL2OSLSLO2L90.000.03
CLCTL1SLO2L90.000.03
XCTL1CTL2X90.000.83683
XCTL1CTL2X90.000.83683
[ atoms ]
;nameat.nummasschargeptypesigmaepsilon
CL612.011000.62A0.3563594872560.29288
HAL111.0080000.09A0.2351972615890.092048
HAL211.0080000.09A0.2387608564620.117152
[ pairs ]
; ijfuncsigma1-4epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CTL1CTL110.3385415128930.04184
CTL1CTL210.3385415128930.04184
CTL1CTL310.3385415128930.04184

WARNING 141 [file aot_2.itp, line 228]:
  Too few parameters on line (source file toppush.c, line 1248)


WARNING 142 [file aot_2.itp, line 229]:
  Too few parameters on line (source file toppush.c, line 1248)

Excluding 3 bonded neighbours molecule type 'AOT'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file aotwater.top, line 19]:
  System has non-zero total charge: -1.35e+01

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:60  OTHER residues
There are: 0PROTEIN residues
There are: 0DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 1110 elements
Making dummy/rest group for Acceleration containing 1110 elements
Making dummy/rest group for Freeze containing 1110 elements
Making dummy/rest group for Energy Mon. containing 1110 elements
Making dummy/rest group for VCM containing 1110 elements
Number of degrees of freedom in T-Coupling group rest is 3192.00
Making dummy/rest group for User1 containing 1110 elements
Making dummy/rest group for User2 containing 1110 elements
Making dummy/rest group for XTC containing 1110 elements
Making dummy/rest group for Or. Res. Fit containing 1110 elements
Making dummy/rest group for QMMM containing 1110 elements
T-Coupling   has 1 element(s): rest
Energy Mon.  has 1 element(s): rest
Acceleration has 1 element(s): rest
Freeze   has 1 element(s): rest
User1has 1 element(s): rest
User2has 1 element(s): rest
VCM  has 1 element(s): rest
XTC  has 1 element(s): rest
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file aotwater_min.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 1 Mb of data
writing run input file...

There were 2 notes

There were 142 warnings

---
Program grompp, VERSION 4.0.5
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (142), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
---


I appreciate your answers.

Lum
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Re: [gmx-users] Parameters for neutral phosho-amino acids

[Justin A. Lemkul]

Michael McGovern wrote:
Hi everyone.  I'm doing some simulations of a phosphorylated peptide. 
 Right now, I'm using the amber force field with some parameters that 
were obtained for charged phosphorylated amino acids in a paper I found. 
 Now I want to simulate uncharged phosphate groups, but the paper only 
gave parameters for -1 and -2 charge states.  I'm stuck on this.  I'm 
only missing two bond parameters.  They are the OH-P-OH angle and the 
HO-OH-P-OH dihedral, where the atom type names are shown below:




A quick look at ffamber99bon.itp gives:

O2  P   OH   1   108.230376.560 ;
O2  P   O2   1   119.900   1171.520 ;
O2  P   OS   1   108.230836.800 ;
OH  P   OS   1   102.600376.560 ;
OS  P   OS   1   102.600376.560 ;

Are none of these appropriate?

As for dihedrals, from ffamber99bon.itp:

X   OH  P   X 3 1.04600 3.13800 0.0-4.18400 0.0 
0.0 ; JCC,7,(1986),230
X   OS  P   X 3 1.04600 3.13800 0.0-4.18400 0.0 
0.0 ; JCC,7,(1986),230


Perhaps that reference will have more information as far as the suitability of 
these parameters.



   O2 (-)
   | |
R-P-OH-HO
   | |
  O2
(-1 charge)

   O2
   | |
R-P-OH-HO
|
   OH
|
   HO
(neutral)

Is there some way of getting these parameters?  Once that is done, I 
still would need to assign charges.  Does anyone have any idea what the 
best way forward would be?  I would prefer to stay in the amber force 
field, but if that's not possible I'm open to others.




Using antechamber is your best bet.  See the relevant discussions within the 
last day or so (and in the list archive) about using antechamber with acpypi.


There are parameters for Gromos96 43a1 (Ser, Thr, Tyr in -1 and -2 forms), 
published some time ago in J. Mol. Biol.  These files were provided on the 
GROMACS site in the User Contributions section, but were formatted for use with 
version 3.1.4.  I re-formatted them and have them available if you want to use 
them under version 4.0.x.  Just contact me off-list and I will send you the tarball.


-Justin


Thanks for your time!


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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] Parameters for neutral phosho-amino acids

[Michael McGovern]

Hi everyone.  I'm doing some simulations of a phosphorylated peptide.  Right 
now, I'm using the amber force field with some parameters that were obtained 
for charged phosphorylated amino acids in a paper I found.  Now I want to 
simulate uncharged phosphate groups, but the paper only gave parameters for -1 
and -2 charge states.  I'm stuck on this.  I'm only missing two bond 
parameters.  They are the OH-P-OH angle and the HO-OH-P-OH dihedral, where the 
atom type names are shown below:
   O2 (-)   | |R-P-OH-HO   | |  O2
(-1 charge)
   O2   | |R-P-OH-HO    |   OH    |   HO(neutral)
Is there some way of getting these parameters?  Once that is done, I still 
would need to assign charges.  Does anyone have any idea what the best way 
forward would be?  I would prefer to stay in the amber force field, but if 
that's not possible I'm open to others.
Thanks for your time!

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[gmx-users] parameters for salicylate

[maria goranovic]

Dear All,

Are there any parameters for salicylic acid available which can be used with
the berger force field for lipids or with the OPLS-compatible Berger force
field for lipids ?

thank you for the support

maria

-- 
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Technical University of Denmark
Copenhagen
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Re: [gmx-users] Parameters for membrane stability

[Justin A. Lemkul]

Ragnarok sdf wrote:
I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC 
from tieleman's website as a starting structure. I've run a short 1 ns 
semi-isotropic simulation at 323 K and monitored the area per lipid as a 
stability parameter for my membrane simulation. If the area per lipid 
maintains the same, can I consider my membrane as being stable? Would 
there be better parameters for it?


Many membrane parameters are inter-related, but if you are trying to make a 
strong argument for stability (and ultimately equilibrium behavior), I would 
think a much more thorough analysis would include: deuterium order parameters, 
membrane thickness, and lateral diffusion of lipids, if not a few more.


-Justin


Thank you in advance
Fabrício Bracht




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Justin A. Lemkul
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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] Parameters for membrane stability

[Ragnarok sdf]

I've just generated a 512 DPPC bilayer using genconf with a 128 DPPC from
tieleman's website as a starting structure. I've run a short 1 ns
semi-isotropic simulation at 323 K and monitored the area per lipid as a
stability parameter for my membrane simulation. If the area per lipid
maintains the same, can I consider my membrane as being stable? Would there
be better parameters for it?
Thank you in advance
Fabrício Bracht
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Re: [gmx-users] parameters for Phosphorylated threonine and serine

[Lucio Ricardo Montero Valenzuela]

I also cannot open the ffg43a1p file, using the mozilla firefox download
manager, on Ubuntu Jaunty. Some months ago I could open it in Windows.
Mensaje citado por "Justin A. Lemkul" :

>
>
> nikhil damle wrote:
> > *.tar gives error during extracting saying that it is not a .tar archive.
> >
>
> Works fine for me.  What are you doing to try to open it?
>
> -Justin
>
> > Regards,
> > Nikhil
> >
> > 
> > *From:* Justin A. Lemkul 
> > *To:* Discussion list for GROMACS users 
> > *Sent:* Saturday, 18 July, 2009 9:31:01 PM
> > *Subject:* Re: [gmx-users] parameters for Phosphorylated threonine and
> > serine
> >
> >
> >
> > nikhil damle wrote:
> >  > Hi,
> >  >
> >  > Can anyone suggest me where to get phosphorylated ser and threonine
> > parameters ?
> >  >
> >
> > The ffG43a1p tarball is available under User Contributions on the
> > Gromacs website:
> >
> >
>
http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields
> >
> > As I recall, there were some formatting problems with some of the files
> > (they were made under a very old Gromacs version, and some formatting
> > has since changed).  If you run into problems, you may contact me
> > off-list; I should have the corrected files.
> >
> > -Justin
> >
> >  > Regards,
> >  > Nikhil
> >  >
> >  > 
> >  > Yahoo! recommends that you upgrade to the new and safer Internet
> > Explorer 8
> >
>
<http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/>.
> >  >
> >  >
> >  > 
> >  >
> >  > ___
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> > <mailto:gmx-users@gromacs.org>
> >  > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> > <mailto:gmx-users-requ...@gromacs.org>.
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> >
> > -- 
> >
> > 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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> >
>
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>
> --
> 
>
> 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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>


Lucio Ricardo Montero Valenzuela
Instituto de Biotecnologia, UNAM
Departamento de Biologia Molecular de Plantas
Av. Universidad 2001, Col. Chamilpa
Cuernavaca 62210
Mexico


Este mensaje fue enviado desde el servidor Webmail del Instituto de 
Biotecnologia.
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Re: [gmx-users] parameters for Phosphorylated threonine and serine

[Justin A. Lemkul]

nikhil damle wrote:

*.tar gives error during extracting saying that it is not a .tar archive.



Works fine for me.  What are you doing to try to open it?

-Justin


Regards,
Nikhil


*From:* Justin A. Lemkul 
*To:* Discussion list for GROMACS users 
*Sent:* Saturday, 18 July, 2009 9:31:01 PM
*Subject:* Re: [gmx-users] parameters for Phosphorylated threonine and 
serine




nikhil damle wrote:
 > Hi,
 >
 > Can anyone suggest me where to get phosphorylated ser and threonine 
parameters ?

 >

The ffG43a1p tarball is available under User Contributions on the 
Gromacs website:


http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields

As I recall, there were some formatting problems with some of the files 
(they were made under a very old Gromacs version, and some formatting 
has since changed).  If you run into problems, you may contact me 
off-list; I should have the corrected files.


-Justin

 > Regards,
 > Nikhil
 >
 > 
 > Yahoo! recommends that you upgrade to the new and safer Internet 
Explorer 8 
<http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/>.

 >
 >
 > 
 >
 > ___
 > gmx-users mailing listgmx-users@gromacs.org 
<mailto:gmx-users@gromacs.org>

 > http://lists.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 
<mailto:gmx-users-requ...@gromacs.org>.

 > Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 

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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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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Re: [gmx-users] parameters for Phosphorylated threonine and serine

[nikhil damle]

*.tar gives error during extracting saying that it is not a .tar archive. 

Regards,
Nikhil





From: Justin A. Lemkul 
To: Discussion list for GROMACS users 
Sent: Saturday, 18 July, 2009 9:31:01 PM
Subject: Re: [gmx-users] parameters for Phosphorylated threonine and serine



nikhil damle wrote:
> Hi,
> 
> Can anyone suggest me where to get phosphorylated ser and threonine 
> parameters ?
> 

The ffG43a1p tarball is available under User Contributions on the Gromacs 
website:

http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields

As I recall, there were some formatting problems with some of the files (they 
were made under a very old Gromacs version, and some formatting has since 
changed).  If you run into problems, you may contact me off-list; I should have 
the corrected files.

-Justin

> Regards,
> Nikhil
> 
> 
> Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 
> <http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/>.
> 
> 
> 
> 
> ___
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-- 

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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Re: [gmx-users] parameters for Phosphorylated threonine and serine

[Justin A. Lemkul]

nikhil damle wrote:

Hi,

Can anyone suggest me where to get phosphorylated ser and threonine 
parameters ?




The ffG43a1p tarball is available under User Contributions on the Gromacs 
website:

http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Force_fields

As I recall, there were some formatting problems with some of the files (they 
were made under a very old Gromacs version, and some formatting has since 
changed).  If you run into problems, you may contact me off-list; I should have 
the corrected files.


-Justin


Regards,
Nikhil


Yahoo! recommends that you upgrade to the new and safer Internet 
Explorer 8 
.





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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] parameters for Phosphorylated threonine and serine

[nikhil damle]

Hi,

Can anyone suggest me where to get phosphorylated ser and threonine parameters ?

Regards,
Nikhil



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[gmx-users] parameters of Fe-S cluster

[subarna thakur]

Hello
Does anyone have the topology parameters for Fe-S cluster ?

Subarna


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Re: [gmx-users] Parameters for -Si-Si- chains?

[Florian Dommert]

* Semen Esilevsky  [2009-06-23 06:06:58 -0700]:



ThanksTsjerk, Google is definitely our best friend :) However, digging for 
parameters and testing the funny mixed force field is not justified in this 
case - the project is small as well as the amount of financing :) So, I whould 
be very grateful if somebody could point me to the ready-to-use -Si-Si- GROMACS 
topologies (if they exists of course).


Mixing force field parameters is very dangerous, because they are
parametrized in respect to each other, therefore I am quite sure that
Tserk did not meant that you should mix any parameters. The choice of a
suitable set of parameters depends on many factors, the environment you
simulate, the boundary conditions, temperature ... . So I interpret
Tsjerks reply in the following way: literature should be searched to find a 
reference
article describing the simulation of a very similar system, from this
reference a consistent force field should derived and applied in your
simulation.

Flo





- Original Message 
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Tuesday, June 23, 2009 11:22:39 AM
Subject: Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:

Dear All,
Our colleges asked me to do some rather simple MD of the organic-silicone
compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
not so simple because of the force field. Does anybody know about parameters
for such systems, which are adapted for GROMACS? I've only found -Si-O-
-parameters in standard ffgmx, which is not what I need. OPLS also has no
parameters for -Si-Si-Si- chains. Probably somebody know about other force
fields from which it is possible to transfer missed parameters?

Regards,
Semen


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--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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--
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Dipl.-Phys.

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Tel: +49 - 711 / 6856-3613
Fax: +49 - 711 / 6856-3658

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Re: [gmx-users] Parameters for -Si-Si- chains?

[Semen Esilevsky]

ThanksTsjerk, Google is definitely our best friend :) However, digging for 
parameters and testing the funny mixed force field is not justified in this 
case - the project is small as well as the amount of financing :) So, I whould 
be very grateful if somebody could point me to the ready-to-use -Si-Si- GROMACS 
topologies (if they exists of course).



- Original Message 
From: Tsjerk Wassenaar 
To: Discussion list for GROMACS users 
Sent: Tuesday, June 23, 2009 11:22:39 AM
Subject: Re: [gmx-users] Parameters for -Si-Si- chains?

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:
> Dear All,
> Our colleges asked me to do some rather simple MD of the organic-silicone
> compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
> not so simple because of the force field. Does anybody know about parameters
> for such systems, which are adapted for GROMACS? I've only found -Si-O-
> -parameters in standard ffgmx, which is not what I need. OPLS also has no
> parameters for -Si-Si-Si- chains. Probably somebody know about other force
> fields from which it is possible to transfer missed parameters?
>
> Regards,
> Semen
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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Re: [gmx-users] Parameters for -Si-Si- chains?

[Tsjerk Wassenaar]

Hi Semen,

When confronted with Si-Si-Si and radicals in the same sentence, I
don't get comforted and definitely wouldn't characterize it as 'rather
simmple' ;)
There seem to be quite a number of publications referring to MD of
Si-Si systems though. Try googling a bit, or try Web of Science; gives
quite a number of hits which you could use to extract parameters.
However, do try to assess how reasonable the assumptions/calculations
in these papers are for determining the parameters.

Cheers,

Tsjerk

On Tue, Jun 23, 2009 at 9:51 AM, Semen Esilevsky wrote:
> Dear All,
> Our colleges asked me to do some rather simple MD of the organic-silicone
> compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be
> not so simple because of the force field. Does anybody know about parameters
> for such systems, which are adapted for GROMACS? I've only found -Si-O-
> -parameters in standard ffgmx, which is not what I need. OPLS also has no
> parameters for -Si-Si-Si- chains. Probably somebody know about other force
> fields from which it is possible to transfer missed parameters?
>
> Regards,
> Semen
>
>
> ___
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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[gmx-users] Parameters for -Si-Si- chains?

[Semen Esilevsky]

Dear All,
Our colleges asked me to do some rather simple MD of the organic-silicone 
compounds (-Si-Si-Si- backbone with organic radicals), but it appeared to be 
not so simple because of the force field. Does anybody know about parameters 
for such systems, which are adapted for GROMACS? I've only found -Si-O- 
-parameters in standard ffgmx, which is not what I need. OPLS also has no 
parameters for -Si-Si-Si- chains. Probably somebody know about other force 
fields from which it is possible to transfer missed parameters?

Regards,
Semen



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Re: [gmx-users] Parameters

[Xavier Periole]

On Mon, 10 Nov 2008 00:45:19 +
 "andrea hanna" <[EMAIL PROTECTED]> wrote:

Dear users,

I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and
the following parameters (only a few are given):

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 125000
comm-mode= Linear
nstcomm  = 1

nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no

coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.0

I recently noticed from the manual that the nstlist should be 5 with gromos
96 ff. I have a couple of questions.
1. should this be 5 with a 0.001 timestep or with a 0.002 timestep
2. As I have done a lot of work using these parameters I was really looking
for some suggestions/advice as to whether I can use any of my data - I;m
really clinging onto hope here! And as to how 'badly' this choice/mistake
will have affected my work.

The nstlist is one issue but the most worrying is the use of a straight
cutoff at 1.0 nm for the vdW. This should be 1.4 nm and makes a big 
difference.


Note also that I am not sure this force field has not been tested for PME and
developed for Reaction-Field. You should check the original paper.

You can rerun some of your jobs with a parameter set closer to the original
and check whether your observable vary significantly or not. That is
probably the best you can do.

XAvier.


Thanks,
Les


-
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-
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[gmx-users] Parameters

[andrea hanna]

Dear users,

I have performed a number of simulations using the ffG43a2 ff in 3.2.1 and
the following parameters (only a few are given):

; RUN CONTROL PARAMETERS
integrator   = md
tinit= 0
dt   = 0.002
nsteps   = 125000
comm-mode= Linear
nstcomm  = 1

nstlist  = 10
ns-type  = Grid
pbc  = xyz
rlist= 1.0
domain-decomposition = no

coulombtype  = PME
rcoulomb-switch  = 0
rcoulomb = 1.0
epsilon-r= 1
vdw-type = Cut-off
rvdw-switch  = 0
rvdw = 1.0

I recently noticed from the manual that the nstlist should be 5 with gromos
96 ff. I have a couple of questions.
1. should this be 5 with a 0.001 timestep or with a 0.002 timestep
2. As I have done a lot of work using these parameters I was really looking
for some suggestions/advice as to whether I can use any of my data - I;m
really clinging onto hope here! And as to how 'badly' this choice/mistake
will have affected my work.

Thanks,
Les
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Re: [gmx-users] Parameters for DNA bases

[TJ Piggot]

If you really want to use OPLS/AA then you can find DNA parameters on the 
Gromacs website using the following link.


http://www.gromacs.org/component/option,com_docman/task,doc_details/gid,45/Itemid,26/

However i am not sure that these parameters are well tested and i am not 
sure if they have been used in many/any published works. Like Justin said 
the AMBER forcefields would be a better option unless you need OPLS/AA for 
a specific reason, for more info on the AMBER forcefields in Gromacs see:


http://chemistry.csulb.edu/ffamber/

Hope this helps

Tom

--On Tuesday, September 02, 2008 21:24:45 -0400 "Justin A. Lemkul" 
<[EMAIL PROTECTED]> wrote:





Jeff Woodford wrote:

Hi all,

Forgive me if this is a stupid question, but:

I am attempting to simulate the interaction between a peptide and a DNA
strand using the OPLS/AA force field.  However the parameters for the
DNA bases don't appear to be included.  Where might I find these
parameters suitable for adapting to GROMACS?




Any particular motivation for using OPLS-AA?  The AMBER force fields
include both DNA and protein.

-Justin



Thanks in advance,

-Jeff



Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873






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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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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] Parameters for DNA bases

[Justin A. Lemkul]

Jeff Woodford wrote:

Hi all,

Forgive me if this is a stupid question, but:

I am attempting to simulate the interaction between a peptide and a DNA 
strand using the OPLS/AA force field.  However the parameters for the 
DNA bases don’t appear to be included.  Where might I find these 
parameters suitable for adapting to GROMACS?


 


Any particular motivation for using OPLS-AA?  The AMBER force fields include 
both DNA and protein.


-Justin



Thanks in advance,

-Jeff

 


Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873

 





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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] Parameters for DNA bases

[Jeff Woodford]

Hi all,

Forgive me if this is a stupid question, but:

I am attempting to simulate the interaction between a peptide and a DNA
strand using the OPLS/AA force field.  However the parameters for the DNA
bases don't appear to be included.  Where might I find these parameters
suitable for adapting to GROMACS?

 

Thanks in advance,

-Jeff

 

Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873

 

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[gmx-users] parameters for protonated nitrogen

[Samuel Coulbourn Flores 花山]

Hi Guys,

I have a molecule with a nitrogen bonded to three carbons and one  
proton.  Can anyone tell me what parameters to use?  I have looked  
through the amber parameter file and can't find suitable parameters.   
I'm not sure if it is probable, but if the N1 of cytidine were  
protonated, it would be similar to my situation.


Many thanks,

Sam



On Sep 26, 2007, at 3:27 AM, [EMAIL PROTECTED] wrote:


Thanks for your help Alan, Yang, and Belquis!

Now I managed to get trajectory in which a droplet stays in the  
middle of the simulation box while a surface moves below the  
droplet. First I used trjconv to remove periodicity (-pbc nojump)  
and then performed translational fit for the droplet (-fit  
translational) and finally transferred all the translating surface  
atoms back to the simulation box (-pbc -inbox).


However, there is still a problem with fitting procedure which is  
performed in three dimension and hence the surface translates  
upwards during the video. It should be quite easy to modify trjconv  
so that the fitting is performed only for the xy coordinates (not  
for the z coordinate perpendicular to the surface) but with my  
programming skills I wasn't able to do that (actually I wasnt able  
to find the correct lines). So I would like to know if someone has  
made a such modification to trjconv (trjconv_d) or could help me to  
do it?


Thanks,

Janne



Hello Janne,

this is what I usually do when my molecules cross the box or dance  
all

around and it works for me:

I first do this with the "original" unmodified or fitted xtc or trr  
file:


trjconv -f  -o  -pbc nojump

then i take the modified trr or xtc and do a fit:

trjconv -f -s -fit rot+trans


Belquis



Hello gmx-users!

I am trying to make a simulation video in which a water droplet is
rolling or sliding on a surface. Due to a periodic boundary  
conditions

a droplet is not whole all the time but it disappears from the right
and appears from the left in cycles.

I think that I could create more visual video by removing the  
lateral

motion of the center of mass of a droplet so that the droplet would
stay whole
in the middle of simulation window and the surface would translate
below the droplet. I am not exactly sure how realistic this kind of
video would be and would like to know if someone has better ideas?

If there are no better ideas I would need advices to be able to  
create

a such trajectory or video. Right now I am struggling with trjconv
which might be suitable for this purpose. However, if I use the
droplet as a group for translational fit (-fit translation) I get
trajectory in which the whole system wanders strangly (laterally  
(the

surface moves first to the left and then back to the right) and also
in perpendicular to the surface due to the lowering of the height of
the center of mass of the droplet during the simulation) and the
droplet wont stay whole in the middle of the box. Any ideas what I  
am

doing wrong or how I would be able to get rid of even this lateral
wandering so that I could at least see how realistic this  
procedure is?



Thanks for your time and help in advance,

Janne


--
Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101  
Joensuu,

FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
--

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Samuel Coulbourn Flores, PhD
Altman Lab
Department of BioEngineering
Stanford University
[EMAIL PROTECTED]
650.644.8416

花山
科学者
生物工学部
スタンフォ一ド大学
スタンフォ一ド、カリフォルニア、米国


















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RE: [gmx-users] Parameters of Gold

[Dallas B. Warren]

Some notes here for you as well:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, every problem begins to resemble
a nail. 
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Re: [gmx-users] Parameters of Gold

[David van der Spoel]

rohit gole wrote:

Dear Sir,
Please help me for this problem.

I want to study a protein with a gold surface and I already have the PDB 
file of the surface but when I am running it in Gromacs, its giving an 
fatal error that Gold is not in the residue database. I guess, there are 
no parameters available in the Gromacs. Can someone please tell me what 
all parameters I need to involve?

I am very new to this software.
I will appreciate if someone help me out.

Thanks in advance

read literature for gold parameters compatible with protein force fields.

--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] Parameters of Gold

[rohit gole]

Dear Sir,
Please help me for this problem.

I want to study a protein with a gold surface and I already have the PDB file 
of the surface but when I am running it in Gromacs, its giving an fatal error 
that Gold is not in the residue database. I guess, there are no parameters 
available in the Gromacs. Can someone please tell me what all parameters I need 
to involve?
I am very new to this software.
I will appreciate if someone help me out.

Thanks in advance

Rohit





   
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[gmx-users] parameters of hydrogen peroxide H2O2

[Jochen Hub]

Dear gmx-users,

does anyone know if there are reasonable parameters for hydorgen 
peroxide H2O2 around? I found few references that present parameters for 
H2O2 via google, but in none of the cases it was clear to me where the 
parameters come from exactly and whether they have been tested properly.


Thanks a lot in advance,
Jochen

--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
 


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Re: [gmx-users] parameters for nitric oxide (NO)

[Anthony Cruz]

Hi Jochen:
Did you receive any responce??? I font 2 different parameters for NO.  one of 
2 sites and other of three sites. I try to build the three sithe model but I 
can get it to work because I have problems with the third site, a dummy atom.
Probably you have more experience with GROMACS than me. If you or any one else 
could resolve the problem and help me I will appreciate it.

2 site model : j biol. chem 266 (1993) 17908
3 site model : biophys chem 98 (2002) 183

Anthony


On Tuesday 20 February 2007 8:57 am, Jochen Hub wrote:
> Dear gromacs users,
>
> does anyone know if there are parameters for nitric oxide (NO) published
> somewhere?
>
> Thanks in advance,
> jochen
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[gmx-users] parameters for nitric oxide (NO)

[Jochen Hub]

Dear gromacs users,

does anyone know if there are parameters for nitric oxide (NO) published 
somewhere?


Thanks in advance,
jochen

--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
 


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Re: [gmx-users] parameters for Mn2+

[lieven]

This is the message I originally posted in 2002:

--
  I have been looking again at the Lennard-Jones
parameters (C6 and C12) I tried to derive from
the MM3 force field epsilon and sigma values for
manganese (Mn2+). 

  First of all, I compared the MM3-derived values
for calcium (C6=1.014e-3 kJ.nm**6/mol; C12=4.579e-7
kJ.nm**12/mol) with the values defined in
ffgmxnb.itp (C6=0.10052E-02; C12=0.49800E-06).
The potential functions are plotted in red (MM3-
derived) and green (ffgmxnb.itp). The curves are
very similar. The minimum energy is slightly higher
for the MM3-derived values.
  The blue curve is the potential for the values
I calculated for manganese from the MM3 values
(C6=5.848e-4; C12=6.631e-8).

  Next, I calculated the positions of the energy
minima (sixth root of (2*C12)/C6):
  
                                 r_min (nm)
        calcium, ffgmxnb.itp        0.316
        calcium, MM3-derived        0.311
        manganese, MM3-derived      0.247

  I then tried to compare this with published
van der Waals and ionic radii, but so far this 
is very confusing. The ionic radius for Mn2+
in an octahedral coordination is 0.110 nm. 
The corresponding value for Ca2+ is 0.126 nm.

  Now I will check if the manganese binding site
maintains the correct geometry during a dynamics
run with these parameters.
--

The stability of the coordination turned out to be OK. I 
never got round to my complete in-depth study of sugar 
binding by this metalloprotein, though :-) .

-- 
Lieven Buts
Department of Ultrastructure
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[gmx-users] parameters for Mn2+

[andrea spitaleri]

Hi all,
I need to carry out a simulation with Mn2+ and I found in the mailing list that someone has already 
calculated the parameters for this cation:


http://www.gromacs.org/pipermail/gmx-users/2003-February/004448.html

unfortunately it seems not anymore available in the archive.
Any help or even suggestions for dealing with Mn2+??

Thanks in advance

Andrea


--
---
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
---


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[gmx-users] Parameters for unnatural amino acid F-Phe

[Vanessa Oklejas]

Hi,

I am trying to model a protein that contains 
4-fluoro-phenylalanine.  I've generated an entirely new set of 
parameters (using the Generalized Atom Force Field) to use in gromacs.


I understand that I need to modify the .rtp file and aminoacid.dat 
files in order to obtain a .top file for the pdb structure (pdb2gmx). 
However it isn't clear to me whether I should modify the 
ff_bonded.itp or ff_non_bonded.itp files with my new parameters?


Alternatively, I could simply use the old force field parameters (in 
my case ffamber99) and simply change the para H to an F atom. Would I 
do this modification for both the .rtp and ffamber_bonded.itp files only?


Any ideas would be helpful.

Thanks,
Vanessa

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[gmx-users] parameters for s-AAPF-pNA

[Yujie Wu]

Hi,

I am looking force field parameters for a small peptide: succinyl-Ala-
Ala-Pro-Phe-p-nitroanilide (s-AAPF-pNA). The most troublesome part is
the -pNA residue, for which I have been searching for its partial
charges for a couple of days, but without luck. Does anyone have any
information about the force field parameters for -pNA? Many thanks.

Yujie



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Re: [gmx-users] Parameters for OPLS

[Jochen Hub]

Kobi wrote:


Hello,

I'm equilibrating a Barnase/Barstar complex using OLPS Force Field, but 
I'm not sure which parameters I should use for PME. at the moment I'm 
using the following parameters:


coulombtype = PME
fourierspacing = 0.12
pme_order = 4
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0

Temperature Coupling ist turne on (berendsen) and Pressure Coupling is 
turend off. The size of the box is  4x5.8x10 nm.


thanks 
Kobi


 



These are pretty much standart parameters, so they should be fine...

--

Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de



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[gmx-users] Parameters for OPLS

[Kobi]

Hello,

I'm equilibrating a Barnase/Barstar complex using OLPS Force Field, but 
I'm not sure which parameters I should use for PME. at the moment I'm 
using the following parameters:

coulombtype = PME
fourierspacing = 0.12
pme_order = 4
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0

Temperature Coupling ist turne on (berendsen) and Pressure Coupling is 
turend off. The size of the box is  4x5.8x10 nm.

thanks 
Kobi

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