Re: [gmx-users] after genbox

[Tsjerk Wassenaar]

Hi Nur,

80:20 is equal to four liters to one. One liter of water is 55.4 mole. If
you know how many moles of the other goes into four liters, divide the
number by 55.4 and you know how many you need to add per water molecule.
Then multiply by the number of water molecules to know the number of
molecules to ADD. If you're going to replace, you have to make a
correction. But it's pretty straightforward math.

Cheers,

Tsjerk



On Wed, Dec 5, 2012 at 4:20 AM, Nur Syafiqah Abdul Ghani
wrote:

> Hi guys,
>
> I'm doing simulation with mix-solvent which is hexafluoroisopropaonol
> and water and it needs percentage v/v.The percentage for the ration is
> 80% of hfip and 20% water..
> I already put the solvent by using using the command
>
> genbox -cp protein_box.gro -ci hfi.gro -nmol 1000 -cs spc216.gro -p
> control.top -o protein_mix.gro
>
> So,i already got the value and my question is,how i want to calculate
> the percentage of the ratio to make sure the % is the one that i want?
>
> --
> Best Regards,
>
> Nur Syafiqah Abdul Ghani,
> Theoretical and Computational Chemistry Laboratory,
> Department of Chemistry,
> Faculty of Science,
> Universiti Putra Malaysia,
> 43400 Serdang,
> Selangor.
> 013-7188131
> alternative email : syafiqahabdulgh...@gmail.com
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada
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Re: [gmx-users] strange lincs warning with version 4.6

[sebastian]

On 12/04/2012 07:56 PM, Szilárd Páll wrote:

On Tue, Dec 4, 2012 at 5:09 PM, Mark Abrahamwrote:

   

2fs is normally considered too large a time step for stable integration
with only bonds to hydrogen constrained, so your observation of
non-reproducible LINCS warnings is not indicative of some other problem.

Also, if you ran your CPU-only calculations with nstlist=25 then AFAIK this
works fine, but is inefficient.

 

With the verlet scheme when running on GPUs and/or at high parallelization
nstlist = 25, even up to 50 can give higher performance (and this is safe
to do because the buffer is automatically adjusted).

--
Szilárd


   

Mark

On Tue, Dec 4, 2012 at 3:41 PM, sebastian<
sebastian.wa...@physik.uni-freiburg.de>  wrote:

 

On 11/23/2012 08:29 PM, Szilárd Páll wrote:

   

Hi,

On Fri, Nov 23, 2012 at 9:40 AM, sebastian<
sebastian.wa...@physik.uni-**freiburg.de<
 

sebastian.wa...@physik.uni-freiburg.de>>
 

  wrote:



 

Dear GROMCS user,

I installed the git gromacs VERSION 4.6-dev-20121117-7a330e6-dirty on
   

my
 

local desktop


   

Watch out, the dirty version suffix means you have changed something in
the
source.




 

(2*GTX 670 + i7) and everything works as smooth as possible. The
   

outcomes
 

are very reasonable and match the outcome of the 4.5.5 version without
GPU
acceleration. On our


   

What does "outcome" mean? If that means performance, than something is
wrong, you should see a considerable performance increase (PME,
non-bonded,
bondeds have all gotten a lot faster).



 

With outcome I mean the trajectory not the performance.



   
 

cluster (M2090+2*Xeon X5650) I installed the  VERSION
4.6-dev-20121120-0290409. Using the same .tpr file used for runs with
   

my
 

desktop I get lincs warnings that the watermolecules can't be settled.



   

The group kernels have not "stabilized" yet and there have been some
 

fixes
 

lately. Could you please the latest version and check again.


 

I installed the beta1 release and still the water can not be settled.

  Additionally, you could try running our regression tests suite (
   

git.gromacs.org/**regressiontests<
 

http://git.gromacs.org/regressiontests>)
 

to see if at least the tests pass with the
binaries you compiled
Cheers,
 


The test of the nbnxn_pme setup breaks as well after 50 steps (I 
extended the run using tpbconv) with the same lincs warning. (log attached)




--
Szilárd




 

Cheers,

Sebastian


  My .mdp file looks like:
   

   ;
title= ttt
cpp =  /lib/cpp
include = -I../top
constraints =  hbonds
integrator  =  md
cutoff-scheme   =  verlet

;define  =  -DPOSRES; for possition restraints

dt  =  0.002; ps !
nsteps  =  1  \
nstcomm =  25; frequency for center of mass
motion
removal
nstcalcenergy   =  25
nstxout =  10; frequency for writting the
trajectory
nstvout =  10; frequency for writting the
velocity
nstfout =  10; frequency to write forces to
output trajectory
nstlog  =  1; frequency to write the log
   

file
 

nstenergy   =  1; frequency to write energies
   

to
 

energy file
nstxtcout   =  1

xtc_grps=  System

nstlist =  25; Frequency to update the neighbor
list
ns_type =  grid; Make a grid in the box and
   

only
 

check atoms in neighboring grid cells when constructing a new neighbor
rlist   =  1.4; cut-off distance for the
short-range neighbor list

coulombtype =  PME; Fast Particle-Mesh Ewald
electrostatics
rcoulomb=  1.4; cut-off distance for the
   

coulomb
 

field
vdwtype =  cut-off
rvdw=  1.4; cut-off distance for the vdw
field
fourierspacing  =  0.12; The maximum grid spacing for
   

the
 

FFT grid
pme_order   =  6; Interpolation order for PME
optimize_fft=  yes
pbc=  xyz
Tcoupl  =  v-rescale
tc-grps =  System
tau_t   =  0.1
ref_t   =  300

energygrps  =  Protein Non-Protein

Pcoupl  =  no;berendsen
tau_p   =  0.1
compressibility =  4.5e-5
ref_p   =  1.0
nstpcouple=  5
refcoord_scaling=  all
Pcoupltype  =  isotropic
gen_vel =  no;yes
gen_temp=  300
gen_seed=  -1


Thanks a lot

Sebastian
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Re: [gmx-users] force field

[Justin Lemkul]

On 12/4/12 10:22 PM, cuong nguyen wrote:

Dear gmx users,

i have got the coordinate and topol files of nonanol from the server:
http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html

the .gro file was download from option GROMOS87/GROMACS   polar H's
only
and .top file was from
optionGROMACS
[D](topology)

Please let me know the name of this force field?



"GROMOS87/GROMACS" indicates the GROMOS87 force field in GROMACS format.  The 
GROMOS87 force field is deprecated, so you probably shouldn't be using it since 
far better parameter sets exist.  Also note that PRODRG topologies are generally 
very inaccurate.


-Justin

--


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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] Green fluorescent protein's chromophore

[James Starlight]

Dear Gromacs Users!


I'm looking for the model as well as for the pre-paired topology for
any kind of GFP protein with the chromophore group covaletnly bonded
in the interiour of that protein.

Some times ago I've tried to make such models by hands but I've forced
with some difficulties with the integration of the chromophore group
to the existing GROMOS force field parameter files. In that case I had
.itp for the chromophore group made by PRODRG which I've failed to
convert to the rtp and integrate to other files in accordance to the
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

So I'll be very thankfull if any could provide me with such model as
well as suitable topology which I could use as the example for
preparation of my future models :)


Thanks for help

James
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Re: [gmx-users] Green fluorescent protein's chromophore

[bharat gupta]

Hi,

You can refer this paper for the topology
http://pubs.acs.org/doi/abs/10.1021/jp014476w.

---
BHARAT

On Wed, Dec 5, 2012 at 10:14 PM, James Starlight wrote:

> Dear Gromacs Users!
>
>
> I'm looking for the model as well as for the pre-paired topology for
> any kind of GFP protein with the chromophore group covaletnly bonded
> in the interiour of that protein.
>
> Some times ago I've tried to make such models by hands but I've forced
> with some difficulties with the integration of the chromophore group
> to the existing GROMOS force field parameter files. In that case I had
> .itp for the chromophore group made by PRODRG which I've failed to
> convert to the rtp and integrate to other files in accordance to the
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> So I'll be very thankfull if any could provide me with such model as
> well as suitable topology which I could use as the example for
> preparation of my future models :)
>
>
> Thanks for help
>
> James
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Re: [gmx-users] Green fluorescent protein's chromophore

[James Starlight]

Hi Bharat,

That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.


James

2012/12/5 bharat gupta :
> Hi,
>
> You can refer this paper for the topology
> http://pubs.acs.org/doi/abs/10.1021/jp014476w.
>
> ---
> BHARAT
>
> On Wed, Dec 5, 2012 at 10:14 PM, James Starlight 
> wrote:
>
>> Dear Gromacs Users!
>>
>>
>> I'm looking for the model as well as for the pre-paired topology for
>> any kind of GFP protein with the chromophore group covaletnly bonded
>> in the interiour of that protein.
>>
>> Some times ago I've tried to make such models by hands but I've forced
>> with some difficulties with the integration of the chromophore group
>> to the existing GROMOS force field parameter files. In that case I had
>> .itp for the chromophore group made by PRODRG which I've failed to
>> convert to the rtp and integrate to other files in accordance to the
>>
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>
>> So I'll be very thankfull if any could provide me with such model as
>> well as suitable topology which I could use as the example for
>> preparation of my future models :)
>>
>>
>> Thanks for help
>>
>> James
>> --
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Re: [gmx-users] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 11:00 AM, James Starlight wrote:

Hi Bharat,

That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.




I think it would be better if you describe exactly what you need help with.  If 
it's a matter of having parameters in CHARMM format but not Gromacs format, then 
all you need is to follow the manual to implement the parameters.  If you're 
having a specific problem along the way, please describe it fully and 
specifically, otherwise the default response is "everything's in the manual and 
elaborated on at the webpage you already quoted."


-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] Asymmetry in homo dimer simulation

[Justin Lemkul]

On 12/5/12 10:56 AM, Kavyashree M wrote:

Dear users,

I have simulated a homodimer (both the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A differs from chain B
in both the simulations. In one of the temperature (T2) the rmsf of the
protein is supposed to be more compared to the other (T1).

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

But actually i observed that the fluctuation of chain A at T1 resembles
the fluctuation of chain B at T2 (with increased values) and similarly
the fluctuations of chain B at T1 resembles that of chain A fluctuation
at T2 (with increased values).

Is this possible? or is there anything wrong?



Your results would indicate simply that while one protein subunit fluctuates 
more, the other becomes somewhat more rigid.  That's plausible, but perhaps not 
intuitive.  Keep in mind that RMSF is very sensitive to whether or not your 
simulations are actually converged, and a single trajectory under each condition 
is insufficient to make very solid claims about anything.  How long are the 
simulations?  How much of the initial time is being disregarded, and thus how 
long are the equilibrated segments of the simulations?  How different are T1 and T2?


-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] Asymmetry in homo dimer simulation

[Kavyashree M]

Sir,

Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).

As you have mentioned I do not have replicates of simulations
hence only one 50ns simulation per temperature.

And this happened in two proteins that I had simulated both
are form mesophilic origin.

Thank you
Kavya
On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul  wrote:

>
>
> On 12/5/12 10:56 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I have simulated a homodimer (both the chains with same number
>> of amino acids and in same configuration) using gromacs 453 in
>> OPLSAA force field at 2 different temperatures (say T1 and T2). It
>> was noticed that the rms fluctuation of chain A differs from chain B
>> in both the simulations. In one of the temperature (T2) the rmsf of the
>> protein is supposed to be more compared to the other (T1).
>>
>> When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
>> chain B). I observed that it shows opposite behaviour. ie chainB is
>> having increased fluctuation at T1 than at T2.
>>
>> But actually i observed that the fluctuation of chain A at T1 resembles
>> the fluctuation of chain B at T2 (with increased values) and similarly
>> the fluctuations of chain B at T1 resembles that of chain A fluctuation
>> at T2 (with increased values).
>>
>> Is this possible? or is there anything wrong?
>>
>>
> Your results would indicate simply that while one protein subunit
> fluctuates more, the other becomes somewhat more rigid.  That's plausible,
> but perhaps not intuitive.  Keep in mind that RMSF is very sensitive to
> whether or not your simulations are actually converged, and a single
> trajectory under each condition is insufficient to make very solid claims
> about anything.  How long are the simulations?  How much of the initial
> time is being disregarded, and thus how long are the equilibrated segments
> of the simulations?  How different are T1 and T2?
>
> -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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> Support/Mailing_Lists/Searchbefore
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Re: [gmx-users] Asymmetry in homo dimer simulation

[Kavyashree M]

Dear users,

One more question is. Is there a way to prove
my point?

Thank you
Kavya

On Wed, Dec 5, 2012 at 9:43 PM, Kavyashree M  wrote:

> Sir,
>
> Thank you for the reply. Total simulated time is 50ns.
> first 4ns is left and only 4-50ns were considered for
> rmsf calculations. T1 is 300K and T2 is 363K the protein
> being simulated is from Ecoli (mesophilic).
>
> As you have mentioned I do not have replicates of simulations
> hence only one 50ns simulation per temperature.
>
> And this happened in two proteins that I had simulated both
> are form mesophilic origin.
>
> Thank you
> Kavya
>
> On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 12/5/12 10:56 AM, Kavyashree M wrote:
>>
>>> Dear users,
>>>
>>> I have simulated a homodimer (both the chains with same number
>>> of amino acids and in same configuration) using gromacs 453 in
>>> OPLSAA force field at 2 different temperatures (say T1 and T2). It
>>> was noticed that the rms fluctuation of chain A differs from chain B
>>> in both the simulations. In one of the temperature (T2) the rmsf of the
>>> protein is supposed to be more compared to the other (T1).
>>>
>>> When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
>>> chain B). I observed that it shows opposite behaviour. ie chainB is
>>> having increased fluctuation at T1 than at T2.
>>>
>>> But actually i observed that the fluctuation of chain A at T1 resembles
>>> the fluctuation of chain B at T2 (with increased values) and similarly
>>> the fluctuations of chain B at T1 resembles that of chain A fluctuation
>>> at T2 (with increased values).
>>>
>>> Is this possible? or is there anything wrong?
>>>
>>>
>> Your results would indicate simply that while one protein subunit
>> fluctuates more, the other becomes somewhat more rigid.  That's plausible,
>> but perhaps not intuitive.  Keep in mind that RMSF is very sensitive to
>> whether or not your simulations are actually converged, and a single
>> trajectory under each condition is insufficient to make very solid claims
>> about anything.  How long are the simulations?  How much of the initial
>> time is being disregarded, and thus how long are the equilibrated segments
>> of the simulations?  How different are T1 and T2?
>>
>> -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.
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>> http://www.gromacs.org/**Support/Mailing_Lists
>>
>
>
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Re: [gmx-users] Asymmetry in homo dimer simulation

[Justin Lemkul]

On 12/5/12 11:13 AM, Kavyashree M wrote:

Sir,

Thank you for the reply. Total simulated time is 50ns.
first 4ns is left and only 4-50ns were considered for
rmsf calculations. T1 is 300K and T2 is 363K the protein
being simulated is from Ecoli (mesophilic).



I would suggest you compare different, overlapping blocks of time as a further 
assessment of convergence.  What motivated the choice of the 4-50 ns time frame? 
 Simple RMSD stability?  While that may be one way to assess convergence, it is 
not necessarily definitive.  If you analyze your RMSF results over different 
times, i.e. 4-50, 10-50, 20-50, etc, how do they compare?



As you have mentioned I do not have replicates of simulations
hence only one 50ns simulation per temperature.



I would encourage you to run more simulations.  One trajectory is not 
definitive.

-Justin


And this happened in two proteins that I had simulated both
are form mesophilic origin.

Thank you
Kavya
On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul  wrote:




On 12/5/12 10:56 AM, Kavyashree M wrote:


Dear users,

I have simulated a homodimer (both the chains with same number
of amino acids and in same configuration) using gromacs 453 in
OPLSAA force field at 2 different temperatures (say T1 and T2). It
was noticed that the rms fluctuation of chain A differs from chain B
in both the simulations. In one of the temperature (T2) the rmsf of the
protein is supposed to be more compared to the other (T1).

When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
chain B). I observed that it shows opposite behaviour. ie chainB is
having increased fluctuation at T1 than at T2.

But actually i observed that the fluctuation of chain A at T1 resembles
the fluctuation of chain B at T2 (with increased values) and similarly
the fluctuations of chain B at T1 resembles that of chain A fluctuation
at T2 (with increased values).

Is this possible? or is there anything wrong?



Your results would indicate simply that while one protein subunit
fluctuates more, the other becomes somewhat more rigid.  That's plausible,
but perhaps not intuitive.  Keep in mind that RMSF is very sensitive to
whether or not your simulations are actually converged, and a single
trajectory under each condition is insufficient to make very solid claims
about anything.  How long are the simulations?  How much of the initial
time is being disregarded, and thus how long are the equilibrated segments
of the simulations?  How different are T1 and T2?

-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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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] Green fluorescent protein's chromophore

[James Starlight]

Justin,

The GFP protein consist of chromophore group which matured after
folding of that protein. That prostetic group is the cyclized
derivative of the Ser-Tyr-Gly peptide which is the part of the
alpha-helix of that protein surrounded by the beta-barell interiour.

So I want to make simulation of such protein consisted of covalently
bonded prostetic group. I've made parametrisation of that isolated
chromophore but couldn't integrate it into GROMOS force field because
aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
inportant that different mutants of GFP consist of different types of
that chromophores so manual conversion of the ITP to RTP formats in
each cases ( I'd like to simulate different mutants) would be very
routinely.


James

2012/12/5 Justin Lemkul :
>
>
> On 12/5/12 11:00 AM, James Starlight wrote:
>>
>> Hi Bharat,
>>
>> That simulation have been done in charmm program so the convertion
>> from charmm to gromacs would be more routinely for me.
>>
>>
>
> I think it would be better if you describe exactly what you need help with.
> If it's a matter of having parameters in CHARMM format but not Gromacs
> format, then all you need is to follow the manual to implement the
> parameters.  If you're having a specific problem along the way, please
> describe it fully and specifically, otherwise the default response is
> "everything's in the manual and elaborated on at the webpage you already
> quoted."
>
> -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/Search before posting!
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Re: [gmx-users] Asymmetry in homo dimer simulation

[Kavyashree M]

Sir,

Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult. Instead
I have two mesophilic simulations. But Is there any other way
by which I can prove this point?

Thank you
Kavya

On Wed, Dec 5, 2012 at 9:46 PM, Justin Lemkul  wrote:

>
>
> On 12/5/12 11:13 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> Thank you for the reply. Total simulated time is 50ns.
>> first 4ns is left and only 4-50ns were considered for
>> rmsf calculations. T1 is 300K and T2 is 363K the protein
>> being simulated is from Ecoli (mesophilic).
>>
>>
> I would suggest you compare different, overlapping blocks of time as a
> further assessment of convergence.  What motivated the choice of the 4-50
> ns time frame?  Simple RMSD stability?  While that may be one way to assess
> convergence, it is not necessarily definitive.  If you analyze your RMSF
> results over different times, i.e. 4-50, 10-50, 20-50, etc, how do they
> compare?
>
>
>  As you have mentioned I do not have replicates of simulations
>> hence only one 50ns simulation per temperature.
>>
>>
> I would encourage you to run more simulations.  One trajectory is not
> definitive.
>
> -Justin
>
>  And this happened in two proteins that I had simulated both
>> are form mesophilic origin.
>>
>> Thank you
>> Kavya
>> On Wed, Dec 5, 2012 at 9:36 PM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 12/5/12 10:56 AM, Kavyashree M wrote:
>>>
>>>  Dear users,

 I have simulated a homodimer (both the chains with same number
 of amino acids and in same configuration) using gromacs 453 in
 OPLSAA force field at 2 different temperatures (say T1 and T2). It
 was noticed that the rms fluctuation of chain A differs from chain B
 in both the simulations. In one of the temperature (T2) the rmsf of the
 protein is supposed to be more compared to the other (T1).

 When I compare rmsf of chain A at T1 with chain A at T2 (similarly for
 chain B). I observed that it shows opposite behaviour. ie chainB is
 having increased fluctuation at T1 than at T2.

 But actually i observed that the fluctuation of chain A at T1 resembles
 the fluctuation of chain B at T2 (with increased values) and similarly
 the fluctuations of chain B at T1 resembles that of chain A fluctuation
 at T2 (with increased values).

 Is this possible? or is there anything wrong?


  Your results would indicate simply that while one protein subunit
>>> fluctuates more, the other becomes somewhat more rigid.  That's
>>> plausible,
>>> but perhaps not intuitive.  Keep in mind that RMSF is very sensitive to
>>> whether or not your simulations are actually converged, and a single
>>> trajectory under each condition is insufficient to make very solid claims
>>> about anything.  How long are the simulations?  How much of the initial
>>> time is being disregarded, and thus how long are the equilibrated
>>> segments
>>> of the simulations?  How different are T1 and T2?
>>>
>>> -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
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>> >
>>>
>>> ====
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search>> 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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> * Please search the archive at http://www.grom

Re: [gmx-users] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 11:19 AM, James Starlight wrote:

Justin,

The GFP protein consist of chromophore group which matured after
folding of that protein. That prostetic group is the cyclized
derivative of the Ser-Tyr-Gly peptide which is the part of the
alpha-helix of that protein surrounded by the beta-barell interiour.

So I want to make simulation of such protein consisted of covalently
bonded prostetic group. I've made parametrisation of that isolated
chromophore but couldn't integrate it into GROMOS force field because
aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
inportant that different mutants of GFP consist of different types of
that chromophores so manual conversion of the ITP to RTP formats in
each cases ( I'd like to simulate different mutants) would be very
routinely.



I don't know of a way to convert .itp files into .rtp entries, though it could 
probably be done.  The time investment in developing such a script may not be 
worth it, since creating an .rtp entry is rather simple following the guide in 
the manual and existing entries (i.e. amino acids).  The choice (script vs. 
manual effort in a text editor) is up to you.  I've done similar things with 
other people before, so it's certainly possible, though a bit tedious, 
especially for the GFP chromophore since there are lots of atoms involved.  I 
worked with it several years ago and I simply did it by hand using the 
parameters that were suggested to you earlier for CHARMM.


-Justin



James

2012/12/5 Justin Lemkul :



On 12/5/12 11:00 AM, James Starlight wrote:


Hi Bharat,

That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.




I think it would be better if you describe exactly what you need help with.
If it's a matter of having parameters in CHARMM format but not Gromacs
format, then all you need is to follow the manual to implement the
parameters.  If you're having a specific problem along the way, please
describe it fully and specifically, otherwise the default response is
"everything's in the manual and elaborated on at the webpage you already
quoted."

-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] Asymmetry in homo dimer simulation

[Justin Lemkul]

On 12/5/12 11:21 AM, Kavyashree M wrote:

Sir,

Thank you for your suggestions. I decided the cutoff based on
RMSD convergence. I will calculate at different time intervals.
Running multiple simulation is definitely the best suggestion but
due to time and machine constraint it would be difficult. Instead
I have two mesophilic simulations. But Is there any other way
by which I can prove this point?



Not using single trajectories.  Your job is to convince reviewers that your work 
is sound.  A single trajectory is not convincing, at least to any reviewer that 
does his or her homework :)


-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] Asymmetry in homo dimer simulation

[Kavyashree M]

Sir,

Oh! Thanks for good suggestion. Will find a way out.

Kavya

On Wed, Dec 5, 2012 at 9:56 PM, Justin Lemkul  wrote:

>
>
> On 12/5/12 11:21 AM, Kavyashree M wrote:
>
>> Sir,
>>
>> Thank you for your suggestions. I decided the cutoff based on
>> RMSD convergence. I will calculate at different time intervals.
>> Running multiple simulation is definitely the best suggestion but
>> due to time and machine constraint it would be difficult. Instead
>> I have two mesophilic simulations. But Is there any other way
>> by which I can prove this point?
>>
>>
> Not using single trajectories.  Your job is to convince reviewers that
> your work is sound.  A single trajectory is not convincing, at least to any
> reviewer that does his or her homework :)
>
> -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!
> * 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
>
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Re: [gmx-users] Green fluorescent protein's chromophore

[James Starlight]

Justin,


So as I understood such problems might be with all proteins consisted
of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial
way to obtain parametrized models of such proteins with gromacs force
fields if I have itp's of the prostetic groups made by external
software ?


Thanks for help

James

2012/12/5 Justin Lemkul :
>
>
> On 12/5/12 11:19 AM, James Starlight wrote:
>>
>> Justin,
>>
>> The GFP protein consist of chromophore group which matured after
>> folding of that protein. That prostetic group is the cyclized
>> derivative of the Ser-Tyr-Gly peptide which is the part of the
>> alpha-helix of that protein surrounded by the beta-barell interiour.
>>
>> So I want to make simulation of such protein consisted of covalently
>> bonded prostetic group. I've made parametrisation of that isolated
>> chromophore but couldn't integrate it into GROMOS force field because
>> aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
>> inportant that different mutants of GFP consist of different types of
>> that chromophores so manual conversion of the ITP to RTP formats in
>> each cases ( I'd like to simulate different mutants) would be very
>> routinely.
>>
>
> I don't know of a way to convert .itp files into .rtp entries, though it
> could probably be done.  The time investment in developing such a script may
> not be worth it, since creating an .rtp entry is rather simple following the
> guide in the manual and existing entries (i.e. amino acids).  The choice
> (script vs. manual effort in a text editor) is up to you.  I've done similar
> things with other people before, so it's certainly possible, though a bit
> tedious, especially for the GFP chromophore since there are lots of atoms
> involved.  I worked with it several years ago and I simply did it by hand
> using the parameters that were suggested to you earlier for CHARMM.
>
> -Justin
>
>
>>
>> James
>>
>> 2012/12/5 Justin Lemkul :
>>>
>>>
>>>
>>> On 12/5/12 11:00 AM, James Starlight wrote:


 Hi Bharat,

 That simulation have been done in charmm program so the convertion
 from charmm to gromacs would be more routinely for me.


>>>
>>> I think it would be better if you describe exactly what you need help
>>> with.
>>> If it's a matter of having parameters in CHARMM format but not Gromacs
>>> format, then all you need is to follow the manual to implement the
>>> parameters.  If you're having a specific problem along the way, please
>>> describe it fully and specifically, otherwise the default response is
>>> "everything's in the manual and elaborated on at the webpage you already
>>> quoted."
>>>
>>> -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/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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
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Re: [gmx-users] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 11:46 AM, James Starlight wrote:

Justin,


So as I understood such problems might be with all proteins consisted
of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial
way to obtain parametrized models of such proteins with gromacs force
fields if I have itp's of the prostetic groups made by external
software ?



In general, a prosthetic group that is not bound covalently is handled by .itp 
files, anything covalently attached is handled by .rtp entries.  If you have an 
.itp file for a covalently bound compound, then you need to convert it to .rtp 
using the contents of the .itp.  After all, everything we're talking about is 
topological information, just in different formats.


-Justin



Thanks for help

James

2012/12/5 Justin Lemkul :



On 12/5/12 11:19 AM, James Starlight wrote:


Justin,

The GFP protein consist of chromophore group which matured after
folding of that protein. That prostetic group is the cyclized
derivative of the Ser-Tyr-Gly peptide which is the part of the
alpha-helix of that protein surrounded by the beta-barell interiour.

So I want to make simulation of such protein consisted of covalently
bonded prostetic group. I've made parametrisation of that isolated
chromophore but couldn't integrate it into GROMOS force field because
aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
inportant that different mutants of GFP consist of different types of
that chromophores so manual conversion of the ITP to RTP formats in
each cases ( I'd like to simulate different mutants) would be very
routinely.



I don't know of a way to convert .itp files into .rtp entries, though it
could probably be done.  The time investment in developing such a script may
not be worth it, since creating an .rtp entry is rather simple following the
guide in the manual and existing entries (i.e. amino acids).  The choice
(script vs. manual effort in a text editor) is up to you.  I've done similar
things with other people before, so it's certainly possible, though a bit
tedious, especially for the GFP chromophore since there are lots of atoms
involved.  I worked with it several years ago and I simply did it by hand
using the parameters that were suggested to you earlier for CHARMM.

-Justin




James

2012/12/5 Justin Lemkul :




On 12/5/12 11:00 AM, James Starlight wrote:



Hi Bharat,

That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.




I think it would be better if you describe exactly what you need help
with.
If it's a matter of having parameters in CHARMM format but not Gromacs
format, then all you need is to follow the manual to implement the
parameters.  If you're having a specific problem along the way, please
describe it fully and specifically, otherwise the default response is
"everything's in the manual and elaborated on at the webpage you already
quoted."

-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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--


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] Green fluorescent protein's chromophore

[James Starlight]

Justin,


thanks again for explanation. I'll try find other possible more
automatic ways for conversion of the itp to rtps. If I've success I'll
post here :)


James

tin Lemkul :
>
>
> On 12/5/12 11:46 AM, James Starlight wrote:
>>
>> Justin,
>>
>>
>> So as I understood such problems might be with all proteins consisted
>> of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial
>> way to obtain parametrized models of such proteins with gromacs force
>> fields if I have itp's of the prostetic groups made by external
>> software ?
>>
>
> In general, a prosthetic group that is not bound covalently is handled by
> .itp files, anything covalently attached is handled by .rtp entries.  If you
> have an .itp file for a covalently bound compound, then you need to convert
> it to .rtp using the contents of the .itp.  After all, everything we're
> talking about is topological information, just in different formats.
>
> -Justin
>
>
>>
>> Thanks for help
>>
>> James
>>
>> 2012/12/5 Justin Lemkul :
>>>
>>>
>>>
>>> On 12/5/12 11:19 AM, James Starlight wrote:


 Justin,

 The GFP protein consist of chromophore group which matured after
 folding of that protein. That prostetic group is the cyclized
 derivative of the Ser-Tyr-Gly peptide which is the part of the
 alpha-helix of that protein surrounded by the beta-barell interiour.

 So I want to make simulation of such protein consisted of covalently
 bonded prostetic group. I've made parametrisation of that isolated
 chromophore but couldn't integrate it into GROMOS force field because
 aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
 inportant that different mutants of GFP consist of different types of
 that chromophores so manual conversion of the ITP to RTP formats in
 each cases ( I'd like to simulate different mutants) would be very
 routinely.

>>>
>>> I don't know of a way to convert .itp files into .rtp entries, though it
>>> could probably be done.  The time investment in developing such a script
>>> may
>>> not be worth it, since creating an .rtp entry is rather simple following
>>> the
>>> guide in the manual and existing entries (i.e. amino acids).  The choice
>>> (script vs. manual effort in a text editor) is up to you.  I've done
>>> similar
>>> things with other people before, so it's certainly possible, though a bit
>>> tedious, especially for the GFP chromophore since there are lots of atoms
>>> involved.  I worked with it several years ago and I simply did it by hand
>>> using the parameters that were suggested to you earlier for CHARMM.
>>>
>>> -Justin
>>>
>>>

 James

 2012/12/5 Justin Lemkul :
>
>
>
>
> On 12/5/12 11:00 AM, James Starlight wrote:
>>
>>
>>
>> Hi Bharat,
>>
>> That simulation have been done in charmm program so the convertion
>> from charmm to gromacs would be more routinely for me.
>>
>>
>
> I think it would be better if you describe exactly what you need help
> with.
> If it's a matter of having parameters in CHARMM format but not Gromacs
> format, then all you need is to follow the manual to implement the
> parameters.  If you're having a specific problem along the way, please
> describe it fully and specifically, otherwise the default response is
> "everything's in the manual and elaborated on at the webpage you
> already
> quoted."
>
> -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
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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] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 12:29 PM, James Starlight wrote:

Justin,


thanks again for explanation. I'll try find other possible more
automatic ways for conversion of the itp to rtps. If I've success I'll
post here :)



Please do.  I've never heard of any server or program that does it, but in 
reality the conversion would require nothing more than a rather simple Perl program.


-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] Parametrisation of the cyclic nucleotides in Gromos force fields

[Justin Lemkul]

On 12/5/12 12:57 PM, James Starlight wrote:

Dear Gromacs Users!


In one of my study I investigate interactions of the cyclic
nucleotides (cGMP and cAMP) with some cyclic-nucleotide-binding
proteins. I'm modelling that complexes in the gromos 56a7 ff with the
parameters for ligands made by prodrg.  So I'm not quite sure about
correctness of charge distributions of that cyclic nucleotides. E.g
below charges of my mollecule of cGMP (united atom modell) is present.


;   nr  type  resnr resid  atom  cgnr   charge mass
  1 O 1  DRG  O6 7   -0.211  15.9994
  2 C 1  DRG  C6 70.211  12.0110
  3NR 1  DRG  N1 8   -0.360  14.0067
  4 H 1  DRG  H1 80.360   1.0080
  5 C 1  DRG  C2 10.298  12.0110
  6NT 1  DRG  N2 6   -0.830  14.0067
  7 H 1  DRG H22 60.415   1.0080
  8 H 1  DRG H21 60.415   1.0080
  9NR 1  DRG  N3 1   -0.298  14.0067
 10 C 1  DRG  C4 20.210  12.0110
 11 C 1  DRG  C5 20.096  12.0110
 12NR 1  DRG  N7 2   -0.626  14.0067
 13   CR1 1  DRG  C8 2   -0.030  12.0110
 14HC 1  DRG  H8 20.006   1.0080
 15NR 1  DRG  N9 20.179  14.0067
 16   CH1 1  DRG C1* 20.165  13.0190
 17OA 1  DRG O4* 3   -0.176  15.9994
 18   CH1 1  DRG C4* 30.240  13.0190
 19   CH1 1  DRG C5* 30.089  14.0270
 20OA 1  DRG O5* 3   -0.177  15.9994
 21 P 1  DRG PAQ 91.360  30.9738
 22OA 1  DRG OAR 9   -0.797  15.9994
 23OM 1  DRG OAS 9   -1.539  15.9994
 24OA 1  DRG O3* 4   -0.160  15.9994
 25   CH1 1  DRG C3* 40.160  13.0190
 26   CH1 1  DRG C2* 50.150  13.0190
 27OA 1  DRG O2* 5   -0.548  15.9994
 28 H 1  DRG H8M 50.398   1.0080



Have anobody else modelled the same cyclic nucleotides in gromos ff ?


Is there any particular reason you're using Gromos96 instead of say, AMBER or 
CHARMM?  The latter perform significantly better than Gromos.



I'd like to compare my itp's of ligands with another works :)



At quick glance and without knowing what the ligand you've shown actually is, 
the charges look reasonable for the 43A1 parameter set, but I don't know which 
you're trying to actually use - 56A7 doesn't exist as far as I know.  Do you 
mean 53A6 or 54A7?  If so, the charges do not seem right.


-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] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

Justin,

Indeed the force field is the 54a7 ( modiffied version of the 54a6).

The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with the protein-ligand complexes in
charmm ff for instance.

By the way is there any suitable builing blocks (implemented in the
rtp enties of the gromos ff) which could be used for charge
assignment?


James

2012/12/5 Justin Lemkul :
>
>
> On 12/5/12 12:57 PM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>>
>> In one of my study I investigate interactions of the cyclic
>> nucleotides (cGMP and cAMP) with some cyclic-nucleotide-binding
>> proteins. I'm modelling that complexes in the gromos 56a7 ff with the
>> parameters for ligands made by prodrg.  So I'm not quite sure about
>> correctness of charge distributions of that cyclic nucleotides. E.g
>> below charges of my mollecule of cGMP (united atom modell) is present.
>>
>>
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>>   1 O 1  DRG  O6 7   -0.211  15.9994
>>   2 C 1  DRG  C6 70.211  12.0110
>>   3NR 1  DRG  N1 8   -0.360  14.0067
>>   4 H 1  DRG  H1 80.360   1.0080
>>   5 C 1  DRG  C2 10.298  12.0110
>>   6NT 1  DRG  N2 6   -0.830  14.0067
>>   7 H 1  DRG H22 60.415   1.0080
>>   8 H 1  DRG H21 60.415   1.0080
>>   9NR 1  DRG  N3 1   -0.298  14.0067
>>  10 C 1  DRG  C4 20.210  12.0110
>>  11 C 1  DRG  C5 20.096  12.0110
>>  12NR 1  DRG  N7 2   -0.626  14.0067
>>  13   CR1 1  DRG  C8 2   -0.030  12.0110
>>  14HC 1  DRG  H8 20.006   1.0080
>>  15NR 1  DRG  N9 20.179  14.0067
>>  16   CH1 1  DRG C1* 20.165  13.0190
>>  17OA 1  DRG O4* 3   -0.176  15.9994
>>  18   CH1 1  DRG C4* 30.240  13.0190
>>  19   CH1 1  DRG C5* 30.089  14.0270
>>  20OA 1  DRG O5* 3   -0.177  15.9994
>>  21 P 1  DRG PAQ 91.360  30.9738
>>  22OA 1  DRG OAR 9   -0.797  15.9994
>>  23OM 1  DRG OAS 9   -1.539  15.9994
>>  24OA 1  DRG O3* 4   -0.160  15.9994
>>  25   CH1 1  DRG C3* 40.160  13.0190
>>  26   CH1 1  DRG C2* 50.150  13.0190
>>  27OA 1  DRG O2* 5   -0.548  15.9994
>>  28 H 1  DRG H8M 50.398   1.0080
>>
>>
>>
>> Have anobody else modelled the same cyclic nucleotides in gromos ff ?
>
>
> Is there any particular reason you're using Gromos96 instead of say, AMBER
> or CHARMM?  The latter perform significantly better than Gromos.
>
>
>> I'd like to compare my itp's of ligands with another works :)
>>
>
> At quick glance and without knowing what the ligand you've shown actually
> is, the charges look reasonable for the 43A1 parameter set, but I don't know
> which you're trying to actually use - 56A7 doesn't exist as far as I know.
> Do you mean 53A6 or 54A7?  If so, the charges do not seem right.
>
> -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] Parametrisation of the cyclic nucleotides in Gromos force fields

[Justin Lemkul]

On 12/5/12 1:39 PM, James Starlight wrote:

Justin,

Indeed the force field is the 54a7 ( modiffied version of the 54a6).

The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with the protein-ligand complexes in
charmm ff for instance.



Well, you get out what you put in.  A recent paper 
(dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed very 
poorly for simulating nucleic acids.  There are others, but that's just a recent 
one.  If you're choosing a force field because it makes life easy, be prepared 
to defend your results if they are of poor quality or defend a lot of wasted 
time while you re-do the simulations :)


There are servers that produce CHARMM topologies and other programs that will 
convert AMBER topologies into Gromacs format as well.  I would suggest you 
evaluate all the options available.



By the way is there any suitable builing blocks (implemented in the
rtp enties of the gromos ff) which could be used for charge
assignment?



That depends on the functional group.  If it's also found in proteins, yes.  If 
not, then maybe but probably not.


-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] strange lincs warning with version 4.6

[Roland Schulz]

On Wed, Dec 5, 2012 at 4:14 AM, sebastian <
sebastian.wa...@physik.uni-freiburg.de> wrote:

>
>
> The test of the nbnxn_pme setup breaks as well after 50 steps (I
> extended the run using tpbconv) with the same lincs warning. (log attached)
>
> AFAIK, attachment aren't supported by the mailing list. Could you open a
redmine issue and attach it there?
You could also test the latest release-4-6 version from git. There are 2
bug fixes which might be related to the issue you are seeing.

Roland
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Re: [gmx-users] force field

[cuong nguyen]

Thanks for your email Justin.

I remember you answered an email that there is a PRODRG server working with
higher version of Gromos87. Could you show me the link please?

Also could you please give me the advice about other force field for my
simulation? I am working with surfactants like alcohols, CTAB and triton
x45.

Best regards,

Van

On 5 December 2012 20:00, Justin Lemkul  wrote:

>
>
> On 12/4/12 10:22 PM, cuong nguyen wrote:
>
>> Dear gmx users,
>>
>> i have got the coordinate and topol files of nonanol from the server:
>> http://davapc1.bioch.dundee.**ac.uk/prodrg/submit.html
>>
>> the .gro file was download from option GROMOS87/GROMACS   polar H's
>> only
>> >
>>
>> and .top file was from
>> optionGROMACS> xprodrg#DRGGMX.ITP
>> >
>> [D]> 50BEBB0C5FDC78D6/asdl/**DRGGMX.ITP
>> >(topology)
>>
>>
>> Please let me know the name of this force field?
>>
>>
> "GROMOS87/GROMACS" indicates the GROMOS87 force field in GROMACS format.
>  The GROMOS87 force field is deprecated, so you probably shouldn't be using
> it since far better parameter sets exist.  Also note that PRODRG topologies
> are generally very inaccurate.
>
> -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] force field

[Justin Lemkul]

On 12/5/12 8:29 PM, cuong nguyen wrote:

Thanks for your email Justin.

I remember you answered an email that there is a PRODRG server working with
higher version of Gromos87. Could you show me the link please?



The server has changed and is now managed by a company.  I have not used it in 
months; perhaps the interface has changed.  One used to be able to select which 
force field to use.



Also could you please give me the advice about other force field for my
simulation? I am working with surfactants like alcohols, CTAB and triton
x45.



What does a search of the literature tell you?  There are plenty of simulation 
papers regarding alcohols and surfactants.


-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] force field

[cuong nguyen]

Dear Justin,

with alcohols I can find their force field in AMBER or others. However, I
have just got a paper regarding CTAB (
http://pubs.acs.org/doi/abs/10.1021/la302998k). They use Gromos force
field. I am attempting to find the other better one.

Best regards,

Van
On 6 December 2012 09:35, Justin Lemkul  wrote:

>
>
> On 12/5/12 8:29 PM, cuong nguyen wrote:
>
>> Thanks for your email Justin.
>>
>> I remember you answered an email that there is a PRODRG server working
>> with
>> higher version of Gromos87. Could you show me the link please?
>>
>>
> The server has changed and is now managed by a company.  I have not used
> it in months; perhaps the interface has changed.  One used to be able to
> select which force field to use.
>
>
>  Also could you please give me the advice about other force field for my
>> simulation? I am working with surfactants like alcohols, CTAB and triton
>> x45.
>>
>>
> What does a search of the literature tell you?  There are plenty of
> simulation papers regarding alcohols and surfactants.
>
>
> -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] Missing interactions error during alchemical free energy calculation

[hyunjink]

Hi,

I had the following error while I ran alchemical free energy calculation.


A list of missing interactions:
LJC Pairs NB of452 missing  1
  exclusions of  39702 missing  1

Molecule type 'Other_chain_T'
the first 10 missing interactions, except for exclusions:
LJC Pairs NB atoms8   29   global 829


I have searched your previous discussion about this issue and found that
you discussed about this on this error in this March. I saw you suggested
users to use -pd instead of domain decomposition. However, I wonder
whether any more progress on this issue.

Thanks in advance.

Hyunjin.



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Re: [gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

Justin,

Could you provide me with the example of the server where I could
obtain Gromac's itp topologies for the charmm ff? I know many such
servers which could be useful only for preparation systems for NAMD
program.


By the way recently I've made parametrization of my cGMP molecule by
means of ATB server. In the below example you can see that the charge
distribution is differs from the PRODRG example of that molecule which
I've posted yesterday. Does that charge distribution more suitable for
the 54a force field?

[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  chargemasstotal_charge
1NT1_N4H N21   -0.832  14.0067
2 H1_N4HH2210.416   1.0080
3 H1_N4HH2110.416   1.0080  ;  0.000
4NR1_N4H N12   -0.715  14.0067
5 H1_N4H H120.427   1.0080
6 C1_N4H C220.775  12.0110
7NR1_N4H N32   -0.691  14.0067
8 C1_N4H C420.431  12.0110
9NR1_N4H N92   -0.227  14.0067  ;  0.000
   10 C1_N4H C830.220  12.0110
   11HC1_N4HH0130.162   1.0080
   12 O1_N4H O63   -0.556  15.9994
   13 C1_N4H C630.669  12.0110
   14 C1_N4H C530.026  12.0110
   15NR1_N4H N73   -0.521  14.0067  ;  0.000
   16OE1_N4HO4*4   -0.429  15.9994
   17   CH11_N4HC1*40.429  13.0190  ;  0.000
   18   CH11_N4HC4*50.000  13.0190  ;  0.000
   19OA1_N4HO5*6   -0.422  15.9994
   20 P1_N4HPAQ60.971  30.9738
   21OM1_N4HOAR6   -0.613  15.9994
   22OA1_N4HO3*6   -0.382  15.9994
   23OA1_N4HOAS6   -0.617  15.9994
   24 H1_N4HH0360.497   1.0080
   25   CH21_N4HC5*60.319  14.0270
   26   CH11_N4HC3*60.247  13.0190  ; -0.000
   27   CH11_N4HC2*70.200  13.0190
   28OA1_N4HO2*7   -0.614  15.9994
   29 H1_N4HH8M70.414   1.0080  ;  0.000



James

2012/12/5 Justin Lemkul :
>
>
> On 12/5/12 1:39 PM, James Starlight wrote:
>>
>> Justin,
>>
>> Indeed the force field is the 54a7 ( modiffied version of the 54a6).
>>
>> The main reason of using GROMOS ff in that case was the topology of
>> ligands which could be easily created by means of prodrg or ATB. On
>> other hand I've never worked with the protein-ligand complexes in
>> charmm ff for instance.
>>
>
> Well, you get out what you put in.  A recent paper
> (dx.doi.org/10.1002/jcc.23055) showed that Gromos force fields performed
> very poorly for simulating nucleic acids.  There are others, but that's just
> a recent one.  If you're choosing a force field because it makes life easy,
> be prepared to defend your results if they are of poor quality or defend a
> lot of wasted time while you re-do the simulations :)
>
> There are servers that produce CHARMM topologies and other programs that
> will convert AMBER topologies into Gromacs format as well.  I would suggest
> you evaluate all the options available.
>
>
>> By the way is there any suitable builing blocks (implemented in the
>> rtp enties of the gromos ff) which could be used for charge
>> assignment?
>>
>
> That depends on the functional group.  If it's also found in proteins, yes.
> If not, then maybe but probably not.
>
>
> -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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