date:20120918

Hi everybody,
 I want to make two index groups for my protein. The first one should
contain the whole protein except of the residues :
TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80

I tried it with the arguments:
protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80
protein ! res 65 6 7 61 64 80

Both didn't work.

The other index group should only contain the residues:
TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80

Here I tried:
res 6  res 7  res 61  res 64  res 65  res 66

This worked.

So I don't understand why the negation of this command did not work in the
first index group.

Can you please help me?

Thank you,
 Eva

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Re: [gmx-users] make index groups with make_ndx

The selections are boolean (like a search).

So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or 7)

so you probably want something like ! res65 | ! res 6 etc.


On 2012-09-18 10:56:14AM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
 Hi everybody,
  I want to make two index groups for my protein. The first one should
 contain the whole protein except of the residues :
 TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80
 
 I tried it with the arguments:
 protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80
 protein ! res 65 6 7 61 64 80
 
 Both didn't work.
 
 The other index group should only contain the residues:
 TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80
 
 Here I tried:
 res 6  res 7  res 61  res 64  res 65  res 66
 
 This worked.
 
 So I don't understand why the negation of this command did not work in the
 first index group.
 
 Can you please help me?
 
 Thank you,
  Eva
 
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Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
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Re: [gmx-users] make index groups with make_ndx

Thank you very much for your answer.
I managed it now to get the right index groups.

 The selections are boolean (like a search).

 So to include both 6 and 7 you would use 6 | 7 (make the selection of 6 or
 7)

 so you probably want something like ! res65 | ! res 6 etc.


 On 2012-09-18 10:56:14AM +0200,
 reising...@rostlab.informatik.tu-muenchen.de wrote:
 Hi everybody,
  I want to make two index groups for my protein. The first one should
 contain the whole protein except of the residues :
 TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80

 I tried it with the arguments:
 protein ! res 65 ! res 6 ! res 7 ! res 61 ! res 64 ! res 80
 protein ! res 65 6 7 61 64 80

 Both didn't work.

 The other index group should only contain the residues:
 TYR65, Pro6, Phe7, Tyr61, Arg64, Tyr80

 Here I tried:
 res 6  res 7  res 61  res 64  res 65  res 66

 This worked.

 So I don't understand why the negation of this command did not work in
 the
 first index group.

 Can you please help me?

 Thank you,
  Eva

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 ==
 Peter C. Lai  | University of Alabama-Birmingham
 Programmer/Analyst| KAUL 752A
 Genetics, Div. of Research| 705 South 20th Street
 p...@uab.edu  | Birmingham AL 35294-4461
 (205) 690-0808|
 ==

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Re: [gmx-users] LINCS warning in md run

I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.

I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
to the ffbonded file.
And additionally I looked at the protein and made all the residues which
could somehow influence the protein flexible so that eventual clashes can
be repaired.
But still I got the error:

..Step 3612, time 3.612 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.08, max 0.31 (between atoms 975 and 978)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
976979   32.60.0961   0.0960  0.0960

Step 3613, time 3.613 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.001400 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
976979   33.40.0960   0.0959  0.0960
..

Too many LINCS warnings (1000)


I already minimized the protein and everything was fine. There were no
errors:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.7436938e+05
Maximum force =  8.6871973e+03 on atom 979
Norm of force =  7.1224258e+01

gcq#49: You Could Make More Money As a Butcher (F. Zappa)


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.7436938e+05
Maximum force =  8.6871973e+03 on atom 979
Norm of force =  7.1224258e+01


And also during the grompp run there are no errors.
Can you please help me to find out where the problem lies?


Thank you,
 Eva




 On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
 Ah okey. Thank you.
 I will write them.

 Hmm, but the protein is a crystal structure from pdb with a resolution
 of
 1.2. I already added the hydrogen atoms to this structure and there I
 already minimized them and made a md run. And there were no errors. And
 now I only added the phosphate to the minimized structure. So I thought
 that I only had to minimize the phosphate and the residue it bound on.
 Or is there a mistake in my thought here?

 If adding the phosphate resulted in a crash, then clearly that's the
 problem.  I
 don't understand why you would run EM on just the phosphate and keep the
 rest of
 the protein structure frozen.  Again, that potentially prevents clashes
 from
 being resolved.  I don't understand what value there is in only minimizing
 the
 phosphate.

 -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] LINCS warning in md run

On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.
I just added the phosphate manually and so I want to minimize and run a
short MD with it.

I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
to the ffbonded file.
And additionally I looked at the protein and made all the residues which
could somehow influence the protein flexible so that eventual clashes can
be repaired.
But still I got the error:

..Step 3612, time 3.612 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.08, max 0.31 (between atoms 975 and 978)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976979 32.60.0961 0.0960 0.0960

Step 3613, time 3.613 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.001400 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976979 33.40.0960 0.0959 0.0960
..

So what are these atoms? This gives you a hint at the origin of the problem.
Have you followed the troubleshooting advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System?
It covers basically everything anyone would suggest to you for these types of
errors.

Posting an .mdp file would be useful in case you're doing something wrong with
respect to the run parameters.

Too many LINCS warnings (1000)

I already minimized the protein and everything was fine. There were no
errors:

These are results are not fine at all. The maximum force on atom 979 is huge,
and that's what's causing things to spin out of control very early in the MD.

-Justin

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax 10.
Potential Energy = -7.7436938e+05
Maximum force = 8.6871973e+03 on atom 979
Norm of force = 7.1224258e+01

gcq#49: You Could Make More Money As a Butcher (F. Zappa)

And also during the grompp run there are no errors.
Can you please help me to find out where the problem lies?

Thank you,
Eva

On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Ah okey. Thank you.
I will write them.

Hmm, but the protein is a crystal structure from pdb with a resolution
of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the minimized structure. So I thought
that I only had to minimize the phosphate and the residue it bound on.
Or is there a mistake in my thought here?

If adding the phosphate resulted in a crash, then clearly that's the
problem. I
don't understand why you would run EM on just the phosphate and keep the
rest of
the protein structure frozen. Again, that potentially prevents clashes
from
being resolved. I don't understand what value there is in only minimizing
the
phosphate.

-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] LINCS warning in md run

Looks like there is still something clashing with atom 979.
The resulting force after EM was close to 1, which is not very much
minimized at all...

What is atom 979 and what is near it?

On 2012-09-18 01:22:25PM +0200, reising...@rostlab.informatik.tu-muenchen.de 
wrote:
 I need the rest of the structure just as it is now because I want to do
 electrostatic analysis with it.
 I just added the phosphate manually and so I want to minimize and run a
 short MD with it.
 
 I added the dihedraltype of the amber database
 (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
 to the ffbonded file.
 And additionally I looked at the protein and made all the residues which
 could somehow influence the protein flexible so that eventual clashes can
 be repaired.
 But still I got the error:
 
 ..Step 3612, time 3.612 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.08, max 0.31 (between atoms 975 and 978)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 976979   32.60.0961   0.0960  0.0960
 
 Step 3613, time 3.613 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.000237, max 0.001400 (between atoms 976 and 979)
 bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 976979   33.40.0960   0.0959  0.0960
 ..
 
 Too many LINCS warnings (1000)
 
 
 I already minimized the protein and everything was fine. There were no
 errors:
 
 Steepest Descents converged to machine precision in 15 steps,
 but did not reach the requested Fmax  10.
 Potential Energy  = -7.7436938e+05
 Maximum force =  8.6871973e+03 on atom 979
 Norm of force =  7.1224258e+01
 
 gcq#49: You Could Make More Money As a Butcher (F. Zappa)
 
 
 Steepest Descents converged to machine precision in 15 steps,
 but did not reach the requested Fmax  10.
 Potential Energy  = -7.7436938e+05
 Maximum force =  8.6871973e+03 on atom 979
 Norm of force =  7.1224258e+01
 
 
 And also during the grompp run there are no errors.
 Can you please help me to find out where the problem lies?
 
 
 Thank you,
  Eva
 
 
 
 
  On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
  Ah okey. Thank you.
  I will write them.
 
  Hmm, but the protein is a crystal structure from pdb with a resolution
  of
  1.2. I already added the hydrogen atoms to this structure and there I
  already minimized them and made a md run. And there were no errors. And
  now I only added the phosphate to the minimized structure. So I thought
  that I only had to minimize the phosphate and the residue it bound on.
  Or is there a mistake in my thought here?
 
  If adding the phosphate resulted in a crash, then clearly that's the
  problem.  I
  don't understand why you would run EM on just the phosphate and keep the
  rest of
  the protein structure frozen.  Again, that potentially prevents clashes
  from
  being resolved.  I don't understand what value there is in only minimizing
  the
  phosphate.
 
  -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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-- 
==
Peter C. Lai| University of Alabama-Birmingham
Programmer/Analyst  | KAUL 752A
Genetics, Div. of Research  | 705 South 20th Street
p...@uab.edu| Birmingham AL 35294-4461
(205) 690-0808  |
==

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Re: [gmx-users] LINCS warning in md run




On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

I need the rest of the structure just as it is now because I want to do
electrostatic analysis with it.


Another thing worth considering - why do you necessarily need the rest of the 
structure to be identical?  Or perhaps better stated, why do you believe this to 
be the more appropriate model of reality?  Phosphorylation events frequently 
trigger structural changes in the protein, so I see no reason to assume it will 
have no effect on the rest of the structure.  At the very least, you can try a 
normal EM and MD procedure without freezing anything to see if you can 
determine the problem.  If things run normally without freezing, then you know 
that whatever you are doing here is artificial and problematic.


-Justin


I just added the phosphate manually and so I want to minimize and run a
short MD with it.

I added the dihedraltype of the amber database
(http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
to the ffbonded file.
And additionally I looked at the protein and made all the residues which
could somehow influence the protein flexible so that eventual clashes can
be repaired.
But still I got the error:

..Step 3612, time 3.612 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.08, max 0.31 (between atoms 975 and 978)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 976979   32.60.0961   0.0960  0.0960

Step 3613, time 3.613 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000237, max 0.001400 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 976979   33.40.0960   0.0959  0.0960
..

Too many LINCS warnings (1000)


I already minimized the protein and everything was fine. There were no
errors:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.7436938e+05
Maximum force =  8.6871973e+03 on atom 979
Norm of force =  7.1224258e+01

gcq#49: You Could Make More Money As a Butcher (F. Zappa)


Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.7436938e+05
Maximum force =  8.6871973e+03 on atom 979
Norm of force =  7.1224258e+01


And also during the grompp run there are no errors.
Can you please help me to find out where the problem lies?


Thank you,
  Eva





On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Ah okey. Thank you.
I will write them.

Hmm, but the protein is a crystal structure from pdb with a resolution
of
1.2. I already added the hydrogen atoms to this structure and there I
already minimized them and made a md run. And there were no errors. And
now I only added the phosphate to the minimized structure. So I thought
that I only had to minimize the phosphate and the residue it bound on.
Or is there a mistake in my thought here?


If adding the phosphate resulted in a crash, then clearly that's the
problem.  I
don't understand why you would run EM on just the phosphate and keep the
rest of
the protein structure frozen.  Again, that potentially prevents clashes
from
being resolved.  I don't understand what value there is in only minimizing
the
phosphate.

-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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[gmx-users] Hbond-ETH-WATER

2012-09-18 Thread Praveen Kumar Sappidi

Hi all
 Am Simulating Ethanol-water system using Gromacs4.0.7
 the problem is am not able to calculate number of hydrogen bonds in ethanol
and water-ethanol.
 i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
see hydrogen bonding is formed

  am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg

 please help if anyone knows the solution
--
Thanks  Regards
Praveenkumar Sappidi
Research Scholar
Molecular modelling and simulation lab
Chemical Engineering Department
IIT Madras-600036
Chennai,INDIA

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Re: [gmx-users] charge calculation........

2012-09-18 Thread tarak karmakar

Thanks Mark.

I have gone through the link Parameterization of novel molecules and
I see quantum calculations can be handy for this type of charge
calculation (AMBER). So for the unprotonated tyrosine, I am taking two
more amino acids (left and right) and calculating ESP charges of the
tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please
tell me whether I can include the partial charges of all the atoms of
the middle tyrosine (unprotonated) in the aminoacids.rtp file to
simulate the protein ?

Thanks,
Tarak

On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/09/2012 10:01 PM, tarak karmakar wrote:

 Dear All,

   I want to have one of tyrosine residues in my protein to
 be unprotonated. I am using amber force field for the simulation. But
 in aminoacid.rtp there is no entry for the unprotonated one. So I am
 adding it by myself in to the .rtp file. Now I am bit confused with
 the charge of the unprotonated one. How can I calculate the partial
 charges for each and every atoms in  unprotonated tyrosine? Would
 Gaussian/SCF be a good one to deal with this matter? Should I take the
 tyrosine amino acid alone to calculate the charge in Gaussian ?
 Please suggest me the proper method(s) to calculate the charge.


 It varies, but should be determined by the process by which the rest of the
 force field was determined. See
 http://www.gromacs.org/Documentation/How-tos/Parameterization

 Mark
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[gmx-users] why traj.trr appears

2012-09-18 Thread Dr. Vitaly Chaban

Dear All -

I an using the current version of gromacs. Although I have

nstxout  = 0
nstvout  = 0
nstfout  = 0

in the MDP file, the traj.trr file appears during the MD run (and is
quite large). In older versions, there was no traj.trr with such an
input.

Did I miss something, please?


Dr. Vitaly V. Chaban, 430 Hutchison Hall
Dept. Chemistry, University of Rochester
120 Trustee Road, Rochester, NY 14627-0216
THE UNITED STATES OF AMERICA
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Re: [gmx-users] Hbond-ETH-WATER




On 9/18/12 8:08 AM, Praveen Kumar Sappidi wrote:

Hi all
  Am Simulating Ethanol-water system using Gromacs4.0.7
  the problem is am not able to calculate number of hydrogen bonds in ethanol
and water-ethanol.
  i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i can
see hydrogen bonding is formed

   am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg

  please help if anyone knows the solution


You haven't described why the above command failed to produce what you wanted. 
g_hbond should prompt you to choose groups, which should include ethanol and 
water, so you can create plots of ethanol-ethanol, water-water, and 
ethanol-water hydrogen bonds.


-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] why traj.trr appears




On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:

Dear All -

I an using the current version of gromacs. Although I have

nstxout  = 0
nstvout  = 0
nstfout  = 0

in the MDP file, the traj.trr file appears during the MD run (and is
quite large). In older versions, there was no traj.trr with such an
input.

Did I miss something, please?



The above combination should turn off production of a .trr file.  Something 
doesn't add up.  Verify your settings in the .log and/or .tpr file - perhaps 
you've mixed up .mdp files.


-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] LINCS warning in md run

Okey,
 now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.

The mdp file I use for the minimization looks like this:

define  = -DPOSRES
integrator  = steep
emtol   = 10
nsteps  = 1500
nstenergy   = 1
energygrps  = System
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
rlist   = 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
pbc = xyz


the mdp file for the md run looks like this:

define  = -DPOSRES
integrator  = md
dt  = 0.001
nsteps  = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog  = 1000
nstxtcout   = 500
nstenergy   = 5
energygrps  = Protein Non-Protein
nstcalcenergy   = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist   = 0.9
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
gen_vel = yes
gen_temp= 200.0
gen_seed= 
constraints = all-bonds
tcoupl  = V-rescale
tc-grps = Protein  Non-Protein
tau_t   = 0.1 0.1
ref_t   = 298 298
pcoupl  = no



The output of the minimization run is:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.9280412e+05
Maximum force =  1.0772942e+04 on atom 979
Norm of force =  9.6685356e+01




The output of the MD run is:

Step 1031, time 1.031 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001431, max 0.010707 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
976979   81.60.1272   0.0970  0.0960



The atom 979 is the hydrogen atom on the phosphate. There has to be one
hydrogen atoms because it is protonated once. The other atom 976 is the
oxygen atom where the hydrogen atom is bound to.
The bounding parameters for this kind of binding were already there. I
didn't add them.

I already did it for another phosphorylation on another position in this
structure. And here I also got many LINCS errors. And again the problem is
the connection between the hydrogen atom and the oxygen atom.

But I do not understand why.
Can you please help me?!


 On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
 I need the rest of the structure just as it is now because I want to do
 electrostatic analysis with it.

 Another thing worth considering - why do you necessarily need the rest of
 the
 structure to be identical?  Or perhaps better stated, why do you believe
 this to
 be the more appropriate model of reality?  Phosphorylation events
 frequently
 trigger structural changes in the protein, so I see no reason to assume it
 will
 have no effect on the rest of the structure.  At the very least, you can
 try a
 normal EM and MD procedure without freezing anything to see if you can
 determine the problem.  If things run normally without freezing, then you
 know
 that whatever you are doing here is artificial and problematic.

 -Justin

 I just added the phosphate manually and so I want to minimize and run a
 short MD with it.

 I added the dihedraltype of the amber database
 (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p)
 to the ffbonded file.
 And additionally I looked at the protein and made all the residues which
 could somehow influence the protein flexible so that eventual clashes
 can
 be repaired.
 But still I got the error:

 ..Step 3612, time 3.612 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.08, max 0.31 (between atoms 975 and 978)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
  976979   32.60.0961   0.0960  0.0960

 Step 3613, time 3.613 (ps)  LINCS WARNING
 relative constraint deviation after LINCS:
 rms 0.000237, max 0.001400 (between atoms 976 and 979)
 bonds that rotated more than 30 degrees:
   atom 1 atom 2  angle  previous, current, constraint length
  976979   33.40.0960   0.0959  0.0960
 ..

 Too many LINCS warnings (1000)


 I already minimized the protein and everything was fine. There were no
 errors:

 Steepest Descents converged to machine precision in 15 steps,
 but did not reach the requested Fmax  10.
 Potential Energy  = -7.7436938e+05
 Maximum force =  8.6871973e+03 on atom 979
 Norm of force =  7.1224258e+01

 gcq#49: You Could Make More Money As a Butcher (F. Zappa)


 Steepest Descents converged to machine

Re: [gmx-users] Hbond-ETH-WATER




On 9/18/12 8:56 AM, Praveen Kumar Sappidi wrote:

Hi Justin
prompt for calculation i have shown below

  Reading file eth-water60%-production.tpr, VERSION 4.0.7 (single precision)
Note: tpx file_version 58, software version 73
Specify 2 groups to analyze:
Group 0 ( System) has 19412 elements
Group 1 (   ETHH) has  7412 elements
Group 2 (SOL) has 12000 elements
Group 3 (EC1) has  1853 elements
Group 4 (EC2) has  1853 elements
Group 5 ( EO) has  1853 elements
Group 6 ( OW) has  4000 elements
Group 7 ( EH) has  1853 elements
Group 8 (HW1) has  4000 elements
Group 9 (HW2) has  4000 elements
Select a group: 1
Selected 1: 'ETHH'
Select a group: 2
Selected 2: 'SOL'
Checking for overlap in atoms between ETHH and SOL
Calculating hydrogen bonds between ETHH (7412 atoms) and SOL (12000 atoms)
Found 4000 donors and 4000 acceptors
Reading frame   0 time0.000
Will do grid-seach on 15x15x15 grid, rcut=0.35
Reading frame2000 time 4000.000
Average number of hbonds per timeframe 0.000 out of 8e+06 possible



Can you please post your topology for ethanol?  I suspect your atoms are named 
in a way that g_hbond doesn't not recognize, since the number of donors and 
acceptors seem to only correspond to water (12000/3 = 4000).


-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] Re: why traj.trr appears

2012-09-18 Thread Dr. Vitaly Chaban

On Tue, Sep 18, 2012 at 2:43 PM, Justin Lemkul jalem...@vt.edu wrote:


 On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote:

 Dear All -

 I an using the current version of gromacs. Although I have

 nstxout  = 0
 nstvout  = 0
 nstfout  = 0

 in the MDP file, the traj.trr file appears during the MD run (and is
 quite large). In older versions, there was no traj.trr with such an
 input.

 Did I miss something, please?


 The above combination should turn off production of a .trr file.  Something
 doesn't add up.  Verify your settings in the .log and/or .tpr file - perhaps
 you've mixed up .mdp files.

 -Justin



Thanks. You calmed me down. I was thinking that some new keywords had
been added controlling TRAJ.TRR.

I will investigate the contents of my TRR file...






 --
 

 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] LINCS warning in md run




On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:

Okey,
  now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.

The mdp file I use for the minimization looks like this:

define  = -DPOSRES


Restraints during minimization generally restrict motion in the same way that 
freezing does.  Again, this is a potential barrier to sufficient minimization.



integrator  = steep
emtol   = 10
nsteps  = 1500
nstenergy   = 1
energygrps  = System
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
rlist   = 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
pbc = xyz


the mdp file for the md run looks like this:

define  = -DPOSRES
integrator  = md
dt  = 0.001
nsteps  = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog  = 1000
nstxtcout   = 500
nstenergy   = 5
energygrps  = Protein Non-Protein
nstcalcenergy   = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist   = 0.9
coulombtype = PME
rcoulomb= 0.9
rvdw= 0.9
fourierspacing  = 0.12
pme_order   = 4
ewald_rtol  = 1e-5
gen_vel = yes
gen_temp= 200.0
gen_seed= 
constraints = all-bonds
tcoupl  = V-rescale
tc-grps = Protein  Non-Protein
tau_t   = 0.1 0.1
ref_t   = 298 298
pcoupl  = no



The output of the minimization run is:

Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax  10.
Potential Energy  = -7.9280412e+05
Maximum force =  1.0772942e+04 on atom 979
Norm of force =  9.6685356e+01



Note that this outcome is even worse than before.  The maximum force is now over 
10,000.






The output of the MD run is:

Step 1031, time 1.031 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001431, max 0.010707 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
 976979   81.60.1272   0.0970  0.0960




As you should expect.  If you can't get a reasonable minimization, the MD will 
always crash.




The atom 979 is the hydrogen atom on the phosphate. There has to be one
hydrogen atoms because it is protonated once. The other atom 976 is the
oxygen atom where the hydrogen atom is bound to.
The bounding parameters for this kind of binding were already there. I
didn't add them.

I already did it for another phosphorylation on another position in this
structure. And here I also got many LINCS errors. And again the problem is
the connection between the hydrogen atom and the oxygen atom.

But I do not understand why.


Remove all restraints/freezing/whatever in the .mdp file and try the EM again. 
If it still does not converge to a reasonable value, then there are two 
potential problems:


1. The topology is flawed and thus the structure cannot be run stably
2. The structure cannot accommodate phosphate in this location and due to 
unresolvable clashes, the runs fail


-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] Re: gmx-users Digest, Vol 101, Issue 52

2012-09-18 Thread Praveen Kumar Sappidi

Dr Justin
This is my Topolofy file for Ethanol
[ moleculetype ]
; Namenrexcl
Protein 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB   
chargeB  massB
 1  H  1   ETHH EH  1  0.408  1.008   ; qtot 
0.408
 2 OA  1   ETHH EO  1 -0.67415.9994   ; qtot
-0.266
 3CH2  1   ETHHEC1  1  0.266 14.027   ; qtot 0
 4CH3  1   ETHHEC2  2  0 15.035   ; qtot 0

[ bonds ]
;  aiaj functc0c1c2c3
1 2 2gb_1
2 3 2gb_18
3 4 2gb_27

[ pairs ]
;  aiaj functc0c1c2c3
1 4 1 

[ angles ]
;  aiajak functc0c1c2c3
1 2 3 2ga_12
2 3 4 2ga_15

[ dihedrals ]
;  aiajakal functc0c1c2  
 c3c4c5
1 2 3 4 1gd_23

; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif

; Include ethanol topology
#include ethanol.itp


; Include water topology
#include spc.itp

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif



; Include generic topology for ions
#include ions.itp

[ system ]
; Name
GROwing Monsters And Cloning Shrimps in water

[ molecules ]
; Compound#mols
Protein 1
ETHH 1852
SOL  4000
On Tue, 18 Sep 2012 15:00:07 +0200 (CEST), gmx-users-request wrote
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   gmx-users@gromacs.org
 
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 When replying, please edit your Subject line so it is more specific
 than Re: Contents of gmx-users digest...
 
 Today's Topics:
 
1. Hbond-ETH-WATER (Praveen Kumar  Sappidi)
2. Re: charge calculation (tarak karmakar)
3. why traj.trr appears (Dr. Vitaly Chaban)
4. Re: Hbond-ETH-WATER (Justin Lemkul)
5. Re: why traj.trr appears (Justin Lemkul)
6. Re: LINCS warning in md run
   (reising...@rostlab.informatik.tu-muenchen.de)
7. Re: Hbond-ETH-WATER (Justin Lemkul)
 
 --
 
 Message: 1
 Date: Tue, 18 Sep 2012 18:38:41 +0630
 From: Praveen Kumar  Sappidi ch11d...@smail.iitm.ac.in
 Subject: [gmx-users] Hbond-ETH-WATER
 To: gmx-users@gromacs.org
 Message-ID: 20120918120320.m14...@smail.iitm.ac.in
 Content-Type: text/plain; charset=utf-8
 
 Hi all
  Am Simulating Ethanol-water system using Gromacs4.0.7
  the problem is am not able to calculate number of hydrogen bonds in 
 ethanol and water-ethanol. i can see a small peak at 0.24 of Ethanol-
 water RDFs and visually also i can see hydrogen bonding is formed
 
   am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg
 
  please help if anyone knows the solution
 --
 Thanks  Regards
 Praveenkumar Sappidi
 Research Scholar
 Molecular modelling and simulation lab
 Chemical Engineering Department
 IIT Madras-600036
 Chennai,INDIA
 
 --
 
 Message: 2
 Date: Tue, 18 Sep 2012 17:41:31 +0530
 From: tarak karmakar tarak20...@gmail.com
 Subject: Re: [gmx-users] charge calculation
 To: Discussion list for GROMACS users gmx-users@gromacs.org
 Message-ID:
   cagzmootw6jkd6rzgbodkjebzym67d9ejgaprjhnru8n27yz...@mail.gmail.com
 Content-Type: text/plain; charset=ISO-8859-1
 
 Thanks Mark.
 
 I have gone through the link Parameterization of novel molecules 
 and I see quantum calculations can be handy for this type of charge 
 calculation (AMBER). So for the unprotonated tyrosine, I am taking 
 two more amino acids (left and right) and calculating ESP charges of 
 the tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please
 tell me whether I can include the partial charges of all the atoms of
 the middle tyrosine (unprotonated) in the aminoacids.rtp file to
 simulate the protein ?
 
 Thanks,
 Tarak
 
 On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham 
 mark.abra...@anu.edu.au wrote:
  On 17/09/2012 10:01 PM, tarak karmakar wrote:
 
  Dear All,
 
I want to have one of tyrosine residues in my protein to
  be unprotonated. I am using amber force field for the simulation. But
  in aminoacid.rtp there is no entry for the unprotonated one. So I am
  adding it by myself in to the .rtp file. Now I am bit confused with
  the charge of the unprotonated one. How can I calculate the partial

[gmx-users] v-rescale

2012-09-18 Thread mohammad agha

Dear Gromacs Users,

I have doubt about temperature bath coupling (v-rescale). I use this method 
(v-rescale) for my system, and my system is NPT ensemble.
Has it problem? is v-rescale just used for NVT ensemble or it doesn't have 
restriction?

Please help me.
Thank you in advance
Best Regards
Sara

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Re: [gmx-users] Re: gmx-users Digest, Vol 101, Issue 52



Please don't reply to the entire digest.

On 9/18/12 9:09 AM, Praveen Kumar Sappidi wrote:

Dr Justin
This is my Topolofy file for Ethanol
[ moleculetype ]
; Namenrexcl
Protein 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
  1  H  1   ETHH EH  1  0.408  1.008   ; qtot 
0.408
  2 OA  1   ETHH EO  1 -0.67415.9994   ; qtot
-0.266
  3CH2  1   ETHHEC1  1  0.266 14.027   ; qtot 0
  4CH3  1   ETHHEC2  2  0 15.035   ; qtot 0



The atom names are such that g_hbond does not recognize what atoms they are. 
g_hbond guesses donors and acceptors based on whether they are H, N, or O atoms 
and expects the first character of the atom name to be one of these.  Names 
starting with E will be unrecognized.  Rename the atoms and create a new .tpr 
file to run the analysis.


-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] Issue with genbox

2012-09-18 Thread Bharath K. Srikanth

Hi all

While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.

I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was

genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -try 500 -o 32lipids.gro

This gave me 32 lipids in a random configuration, as expected. I also ran
en energy minimization on this configuration, with no problems (the file
32minimised.gro contained the coordinates after minimisation).

However, when I tried solvating the box with course-grained water
molecules using genbox, the added water molecules were formed in a small
box, at the corner of the lipid box region, and not interspersed with the
lipid molecules. The command I used was

genbox -cp 32minimised.gro -cs water.gro -o lipidsandwater.gro -maxsol 192
-vdwd 0.21

What could the problem be?

For reference, the coordinate file of the water molecules used (water.gro)
is given below:

WATER
  400
 1WW1   0.084   3.595   3.359  0.0663  0.0148  0.2032
 2WW2   0.460   2.488   2.882  0.0999 -0.0648 -0.1661
 3WW3   3.165   2.218   0.652 -0.0881 -0.1237 -0.0896
 4WW4   3.295   3.303   2.679 -0.1486 -0.3229  0.1120
 5WW5   1.213   3.294   0.205 -0.1053 -0.1062  0.1014
 6WW6   1.296   1.446   1.188  0.0877 -0.0566 -0.1282
 7WW7   0.811   1.294   1.352  0.1967  0.2199  0.3289
 8WW8   1.802   2.109   0.786 -0.1596 -0.1576 -0.0010
 9WW9   1.477   3.201   3.141 -0.1225  0.0135  0.1267
10WW   10   0.126   0.762   3.104  0.0776 -0.1781 -0.1549 11W 
  W   11   0.888   0.042   2.906  0.1622 -0.2895 -0.1539 12WW   12
  2.582   0.430   1.793  0.0293  0.1399  0.1850 13WW   13   2.231 
 1.301   0.363  0.0119  0.0262 -0.0578 14WW   14   2.801   0.735  
3.454  0.2122 -0.0713 -0.1525 15WW   15   0.167   0.527   2.579
-0.2237 -0.0155 -0.0333 16WW   16   0.266   3.146   3.600  0.0972
-0.2452  0.1849 17WW   17   1.788   2.536   0.332  0.0552  0.0717 
0.1324 18WW   18   0.220   1.319   2.025  0.1433  0.0166 -0.2722
19WW   19   1.113   1.210   3.262  0.4727  0.0172 -0.1323 20W 
  W   20   3.572   1.069   1.761 -0.2059  0.1490 -0.2361 21WW   21
  3.336   2.112   2.620  0.0164  0.2724 -0.2412 22WW   22   1.644 
 1.445   1.647  0.1858 -0.0232 -0.1210 23WW   23   2.190   2.784  
2.016 -0.0310 -0.0346 -0.0709 24WW   24   0.690   2.218   2.248 
0.2468  0.3122  0.0688 25WW   25   0.049   1.746   1.819  0.1395
-0.2593  0.1148 26WW   26   1.085   1.718   3.011  0.1122 -0.2451
-0.0872 27WW   27   3.356   1.501   3.265  0.1578  0.0056  0.1978
28WW   28   0.972   2.945   1.710  0.1559 -0.3802  0.1129 29W 
  W   29   2.093   2.634   2.844 -0.0502 -0.3423 -0.3093 30WW   30
  1.313   1.274   2.069  0.2198  0.0937  0.0394 31WW   31   1.605 
 2.058   1.712  0.1814  0.5446  0.0734 32WW   32   2.602   2.831  
3.560 -0.2065  0.0601 -0.0493 33WW   33   1.681   2.151   3.570
-0.2224 -0.0375 -0.1153 34WW   34   1.662   1.867   3.048  0.1370 
0.0775 -0.0222 35WW   35   0.071   1.258   3.570  0.2232  0.1052
-0.2036 36WW   36   2.903   2.793   3.169 -0.2625 -0.0170 -0.1553
37WW   37   0.484   0.375   1.167  0.0519 -0.1542  0.1676 38W 
  W   38   1.011   2.633   2.166 -0.0727  0.1966 -0.1345 39WW   39
  3.474   2.416   1.456 -0.1824 -0.2669  0.1078 40WW   40   2.887 
 0.816   2.023 -0.1587  0.0574 -0.0220 41WW   41   3.172   0.769  
0.118 -0.4070  0.0521 -0.1165 42WW   42   3.637   1.570   2.424
-0.2147 -0.2476  0.1190 43WW   43   1.604   3.277   2.177  0.1467
-0.1670 -0.0368 44WW   44   3.378   2.743   0.615  0.0989  0.0259 
0.0111 45WW   45   0.507   3.529   0.369  0.1744 -0.3678 -0.4485
46WW   46   0.900   3.575   1.045  0.0173  0.0027 -0.0388 47W 
  W   47   0.697   0.329   2.471  0.0408  0.2341  0.2612 48WW   48
  3.320   1.347   2.746  0.2014 -0.1504 -0.1893 49WW   49   2.725 
 1.769   1.205 -0.1672 -0.0662  0.2345 50WW   50   2.691   1.457  
0.232  0.0327 -0.0493  0.0328 51WW   51   1.899   2.601   2.372 
0.2344  0.1809 -0.0296 52WW   52   1.705   0.931   1.571  0.0388 
0.0230 -0.1394 53WW   53   2.305   3.018   2.565 -0.0847  0.2589
-0.0957 54WW   54   3.176   1.809   0.987  0.0442  0.0113 -0.1133
55WW   55   2.078   0.467   1.003  0.1398  0.2946 -0.0153 56W 
  W   56   0.735   3.161   0.686  0.0416  0.2541 -0.0365 57WW   57
  0.106   0.660   1.285 -0.0736  0.1442  0.4423 58WW   58   2.892 
 1.267   1.759  0.2127  0.0276  0.1395 59WW   59   0.350   2.884  
1.674 -0.3019 -0.1338 -0.0189 60WW   60   1.691   3.234   0.544 
0.0983  0.0110 -0.0495 61WW   61   3.083

Re: [gmx-users] Issue with genbox




On 9/18/12 9:21 AM, Bharath K. Srikanth wrote:

Hi all

While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.

I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was

genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -try 500 -o 32lipids.gro

This gave me 32 lipids in a random configuration, as expected. I also ran
en energy minimization on this configuration, with no problems (the file
32minimised.gro contained the coordinates after minimisation).

However, when I tried solvating the box with course-grained water
molecules using genbox, the added water molecules were formed in a small
box, at the corner of the lipid box region, and not interspersed with the
lipid molecules. The command I used was

genbox -cp 32minimised.gro -cs water.gro -o lipidsandwater.gro -maxsol 192
-vdwd 0.21

What could the problem be?



You have a 20-nm cubic box (huge) and you're telling genbox to add only a 
maximum of 192 water molecules.  Given the constraints imposed, you should only 
expect to see a small fraction of your box solvated.  Remove -maxsol and try again.


-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] Issue with genbox

2012-09-18 Thread Mark Abraham


On 18/09/2012 11:21 PM, Bharath K. Srikanth wrote:

Hi all

While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.

I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was

genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -try 500 -o 32lipids.gro

This gave me 32 lipids in a random configuration, as expected. I also ran
en energy minimization on this configuration, with no problems (the file
32minimised.gro contained the coordinates after minimisation).

However, when I tried solvating the box with course-grained water
molecules using genbox, the added water molecules were formed in a small
box, at the corner of the lipid box region, and not interspersed with the
lipid molecules. The command I used was

genbox -cp 32minimised.gro -cs water.gro -o lipidsandwater.gro -maxsol 192
-vdwd 0.21

What could the problem be?


-cs and -ci work fundamentally differently. -cs is usually only useful 
for near-complete filling of the box by tiling with the -cs file, so 
restricting it to 192 molecules creates your observation.


Mark



For reference, the coordinate file of the water molecules used (water.gro)
is given below:

WATER
   400
  1WW1   0.084   3.595   3.359  0.0663  0.0148  0.2032
  2WW2   0.460   2.488   2.882  0.0999 -0.0648 -0.1661
  3WW3   3.165   2.218   0.652 -0.0881 -0.1237 -0.0896
  4WW4   3.295   3.303   2.679 -0.1486 -0.3229  0.1120
  5WW5   1.213   3.294   0.205 -0.1053 -0.1062  0.1014
  6WW6   1.296   1.446   1.188  0.0877 -0.0566 -0.1282
  7WW7   0.811   1.294   1.352  0.1967  0.2199  0.3289
  8WW8   1.802   2.109   0.786 -0.1596 -0.1576 -0.0010
  9WW9   1.477   3.201   3.141 -0.1225  0.0135  0.1267
10WW   10   0.126   0.762   3.104  0.0776 -0.1781 -0.1549 11W
   W   11   0.888   0.042   2.906  0.1622 -0.2895 -0.1539 12WW   12
   2.582   0.430   1.793  0.0293  0.1399  0.1850 13WW   13   2.231
  1.301   0.363  0.0119  0.0262 -0.0578 14WW   14   2.801   0.735
3.454  0.2122 -0.0713 -0.1525 15WW   15   0.167   0.527   2.579
-0.2237 -0.0155 -0.0333 16WW   16   0.266   3.146   3.600  0.0972
-0.2452  0.1849 17WW   17   1.788   2.536   0.332  0.0552  0.0717
0.1324 18WW   18   0.220   1.319   2.025  0.1433  0.0166 -0.2722
19WW   19   1.113   1.210   3.262  0.4727  0.0172 -0.1323 20W
   W   20   3.572   1.069   1.761 -0.2059  0.1490 -0.2361 21WW   21
   3.336   2.112   2.620  0.0164  0.2724 -0.2412 22WW   22   1.644
  1.445   1.647  0.1858 -0.0232 -0.1210 23WW   23   2.190   2.784
2.016 -0.0310 -0.0346 -0.0709 24WW   24   0.690   2.218   2.248
0.2468  0.3122  0.0688 25WW   25   0.049   1.746   1.819  0.1395
-0.2593  0.1148 26WW   26   1.085   1.718   3.011  0.1122 -0.2451
-0.0872 27WW   27   3.356   1.501   3.265  0.1578  0.0056  0.1978
28WW   28   0.972   2.945   1.710  0.1559 -0.3802  0.1129 29W
   W   29   2.093   2.634   2.844 -0.0502 -0.3423 -0.3093 30WW   30
   1.313   1.274   2.069  0.2198  0.0937  0.0394 31WW   31   1.605
  2.058   1.712  0.1814  0.5446  0.0734 32WW   32   2.602   2.831
3.560 -0.2065  0.0601 -0.0493 33WW   33   1.681   2.151   3.570
-0.2224 -0.0375 -0.1153 34WW   34   1.662   1.867   3.048  0.1370
0.0775 -0.0222 35WW   35   0.071   1.258   3.570  0.2232  0.1052
-0.2036 36WW   36   2.903   2.793   3.169 -0.2625 -0.0170 -0.1553
37WW   37   0.484   0.375   1.167  0.0519 -0.1542  0.1676 38W
   W   38   1.011   2.633   2.166 -0.0727  0.1966 -0.1345 39WW   39
   3.474   2.416   1.456 -0.1824 -0.2669  0.1078 40WW   40   2.887
  0.816   2.023 -0.1587  0.0574 -0.0220 41WW   41   3.172   0.769
0.118 -0.4070  0.0521 -0.1165 42WW   42   3.637   1.570   2.424
-0.2147 -0.2476  0.1190 43WW   43   1.604   3.277   2.177  0.1467
-0.1670 -0.0368 44WW   44   3.378   2.743   0.615  0.0989  0.0259
0.0111 45WW   45   0.507   3.529   0.369  0.1744 -0.3678 -0.4485
46WW   46   0.900   3.575   1.045  0.0173  0.0027 -0.0388 47W
   W   47   0.697   0.329   2.471  0.0408  0.2341  0.2612 48WW   48
   3.320   1.347   2.746  0.2014 -0.1504 -0.1893 49WW   49   2.725
  1.769   1.205 -0.1672 -0.0662  0.2345 50WW   50   2.691   1.457
0.232  0.0327 -0.0493  0.0328 51WW   51   1.899   2.601   2.372
0.2344  0.1809 -0.0296 52WW   52   1.705   0.931   1.571  0.0388
0.0230 -0.1394 53WW   53   2.305   3.018   2.565 -0.0847  0.2589
-0.0957 54WW   54   3.176   1.809   0.987  0.0442  0.0113 -0.1133
55WW   55   2.078   0.467   1.003  0.1398  0.2946 -0.0153 56W
   W   56   0.735   3.161   0.686  0.0416  0.2541 -0.0365 57WW   57
   0.106   0.660   1.285 -0.0736

Re: [gmx-users] v-rescale

2012-09-18 Thread Tsjerk Wassenaar

Hi Sara,

NPT also requires a routine for temperature coupling. What makes you wonder
about the suitability of v-rescale for that? If you check the mdp files
from tutorial stuff, you'll probably encounter the v-rescale method used in
the NpT simulations.

Cheers,

Tsjerk

On Sep 18, 2012 7:12 AM, mohammad agha mra...@yahoo.com wrote:

Dear Gromacs Users,

I have doubt about temperature bath coupling (v-rescale). I use this method
(v-rescale) for my system, and my system is NPT ensemble.
Has it problem? is v-rescale just used for NVT ensemble or it doesn't have
restriction?

Please help me.
Thank you in advance
Best Regards
Sara

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Re: [gmx-users] Regarding Pulling simulation:To study the base flipping of the thymine

2012-09-18 Thread lloyd riggs

Dear All,

Ill give this a shot.  I guess it depends on your entire system (ie protein 
+DNA or just DNA) and what it is you waant to observe.

and example of why answereing becomes complex.  if A) I want to just look at 
say the total delta G,S or H.  I would only need to EQ several starting 
structures of the Thymine in conformation A, then several in conformation B. 
Then allow each to just run for a reasonable amount of time, in an NVT system. 
Then, you can just use the differences from the two to calculate the total 
energy change, but get no pretty curves, just simply a value.  This is 
relativly quick as it is essentially just long EQs.  I have done this, and it 
it fits biochem data from liturature.  But B) However, say you want the curves, 
or to compare positional or distance or other things (ionization, solvation), 
Then you have to take into account what you want to apply force on, ie a 
protein, the DNA as a whole or at varied positions along the bases, etc...and 
then follow the online tutorial for pull simulations.  If you are doing this 
and it is say just DNA, you then have to do dozens of runs, pulling along e
 ach base and holding the other fixed within reason,(like the complement, then 
the two on either direction or more...) most likely at several adjascent 
positions...to get a reflection of the real system.

Hope that helps in some way.  

Stephan Watkins

 Original-Nachricht 
 Datum: Tue, 18 Sep 2012 02:52:46 +
 Von: Christopher Neale chris.ne...@mail.utoronto.ca
 An: gmx-users@gromacs.org gmx-users@gromacs.org
 Betreff: [gmx-users] Regarding Pulling simulation:To study the base flipping 
 of the thymine

 You can do this with the pull code. To do so, you need to define some sort
 of order parameter for which you have the base flipped in at one extreme
 and the base flipped out at the opposite extreme. There are lots of ways to
 do this and, unfortunately, there is no way to know what the best order
 parameter is without first evaluating it. Therefore, I suggest that you start
 with something simple like the distance between the NH of thymine and the
 NH of the paired guanine (assuming that you really have a TG pair). To pick
 the atom pair for the distance restraint, you can ideally look at a
 structure of equilibrium close association and find a pair of heavy atoms 
 that are
 close.
 
 Chris.
 
  -- original message --
 
 I am studying a system which consists of DNA duplex 20 base pairs.
 Actually
 I am interested in studying the base flipping of  the thymine.
 I have the crystal structure of extrahelical DNA  in which thymine is out
 side the helical structure. I want use pulling simulations to bring this
 base from extrahelical to Intrahelical  conformation, is there any way to
 do it in GROMACS pull code. Please see the figure below (link) for
 description.
 http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png
 
 -- 
 Thanks and Regards,
 kartheek,
 -- 
 gmx-users mailing listgmx-users@gromacs.org
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[gmx-users] PDB and XYZ Structure Files in GROMACS

2012-09-18 Thread Lara Bunte

Hello

Is it possible with GROMACS to convert a given .pdb structure file to a .xyz 
structure file? 


Thanks for help
Greetings
Lara

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Re: [gmx-users] PDB and XYZ Structure Files in GROMACS




On 9/18/12 9:58 AM, Lara Bunte wrote:

Hello

Is it possible with GROMACS to convert a given .pdb structure file to a .xyz 
structure file?



http://gromacs.5086.n6.nabble.com/pdb-to-xyz-file-format-td4998284.html

-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] Regarding Pulling simulation:To study the base flipping of the thymine

2012-09-18 Thread Christopher Neale

What you are talking about with conducting only 2 end-state simulations sounds 
like free energy perturbation and
it relies on conformational overlap of the two endstates. I don't think that it 
is going to give correct free energies
here. The reason to do umbrella sampling (US) is to ensure that there is 
conformational overlap. In any event, I would
be very cautious about using a two-state computation like that, even if you 
don't care about the shape of the
curves. As a final note, the shape of the US curves doesn't necessarily give 
you useful information either. The
shape of the curve depends on the pathway and thus the order parameter that you 
chose. It may or may not
be relevant to the most likely path followed in unrestrained simualtions.

Chris.

 -- original message --

Ill give this a shot.  I guess it depends on your entire system (ie protein 
+DNA or just DNA) and what it is you waant to observe.

and example of why answereing becomes complex.  if A) I want to just look at 
say the total delta G,S or H.  I would only need to EQ several starting 
structures of the Thymine in conformation A, then several in conformation B. 
Then allow each to just run for a reasonable amount of time, in an NVT system. 
Then, you can just use the differences from the two to calculate the total 
energy change, but get no pretty curves, just simply a value.  This is 
relativly quick as it is essentially just long EQs.  I have done this, and it 
it fits biochem data from liturature.  But B) However, say you want the curves, 
or to compare positional or distance or other things (ionization, solvation), 
Then you have to take into account what you want to apply force on, ie a 
protein, the DNA as a whole or at varied positions along the bases, etc...and 
then follow the online tutorial for pull simulations.  If you are doing this 
and it is say just DNA, you then have to do dozens of runs, pulling along e
 ach base and holding the other fixed within reason,(like the complement, then 
the two on either direction or more...) most likely at several adjascent 
positions...to get a reflection of the real system.

Hope that helps in some way.  

Stephan Watkins

 Original-Nachricht 
 Datum: Tue, 18 Sep 2012 02:52:46 +
 Von: Christopher Neale chris.neale at mail.utoronto.ca
 An: gmx-users at gromacs.org gmx-users at gromacs.org
 Betreff: [gmx-users] Regarding Pulling simulation:To study the base flipping 
 of the thymine

 You can do this with the pull code. To do so, you need to define some sort
 of order parameter for which you have the base flipped in at one extreme
 and the base flipped out at the opposite extreme. There are lots of ways to
 do this and, unfortunately, there is no way to know what the best order
 parameter is without first evaluating it. Therefore, I suggest that you start
 with something simple like the distance between the NH of thymine and the
 NH of the paired guanine (assuming that you really have a TG pair). To pick
 the atom pair for the distance restraint, you can ideally look at a
 structure of equilibrium close association and find a pair of heavy atoms 
 that are
 close.
 
 Chris.
 
  -- original message --
 
 I am studying a system which consists of DNA duplex 20 base pairs.
 Actually
 I am interested in studying the base flipping of  the thymine.
 I have the crystal structure of extrahelical DNA  in which thymine is out
 side the helical structure. I want use pulling simulations to bring this
 base from extrahelical to Intrahelical  conformation, is there any way to
 do it in GROMACS pull code. Please see the figure below (link) for
 description.
 http://researchweb.iiit.ac.in/~kartheek.p/extrintra.png
 
 -- 
 Thanks and Regards,
 kartheek,
 -- 
 gmx-users mailing listgmx-users at 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-request at gromacs.org.
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Re: [gmx-users] How to generate a .itp file for molecules?




On 9/18/12 10:25 AM, Ali Alizadeh wrote:

Dear All users

How to generate a .itp file for molecules?(for example, CHARMM ff and
alkanes.)



http://swissparam.ch/

-Justin

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[gmx-users] Re: gmx-users Digest, Vol 101, Issue 56

2012-09-18 Thread Ali Alizadeh

Dear Justin

Thank you so much,

Sincerely
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[gmx-users] Residue 'UNK' not found in residue topology database

2012-09-18 Thread SIMONE BROGI

Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this messagge error:
 Residue 'UNK' not found in residue topology database
 this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???
Thanks in advance for answers

Simone

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Brogi Simone M.Sc. Ph.D.
Department of Pharmaceutical and Applied Chemistry
European Research Centre for Drug Discovery and Development
University of Siena
Via Aldo Moro
53100 Siena, Italy
Phone:+39 0577 234366 e-mail: brog...@unisi.it  simonebrogi1...@hotmail.com
web: http://www.bronaldo.it http://www.natsyndrugs.org
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Re: [gmx-users] Residue 'UNK' not found in residue topology database

On 9/18/12 12:42 PM, SIMONE BROGI wrote:

Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this messagge error:
Residue 'UNK' not found in residue topology database
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???

Most ligands are not part of existing force fields. Please consult the
following:

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

http://www.gromacs.org/Documentation/How-tos/Parameterization

http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field

-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] Re: How to generate a .itp file for molecules




On 9/18/12 1:56 PM, Ali Alizadeh wrote:

Dear Justin

Your link did not help me for generate the methane.itp file but generated
my propane.itp file.



I would suggest you contact the developers of SwissParam to understand why it 
did not work.  Likely there are some limitations on what types of molecules are 
acceptable based on their algorithm.


-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] charge calculation........

2012-09-18 Thread Erik Marklund

As mentioned, you should make RESP charges for AMBER parameters. ESP parameters 
are furthermore often a bit bizarre (aliphatic carbons with charge well below 
-1etc.).

Erik

14.11 skrev tarak karmakar:

 Thanks Mark.
 
 I have gone through the link Parameterization of novel molecules and
 I see quantum calculations can be handy for this type of charge
 calculation (AMBER). So for the unprotonated tyrosine, I am taking two
 more amino acids (left and right) and calculating ESP charges of the
 tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please
 tell me whether I can include the partial charges of all the atoms of
 the middle tyrosine (unprotonated) in the aminoacids.rtp file to
 simulate the protein ?
 
 Thanks,
 Tarak
 
 On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham mark.abra...@anu.edu.au wrote:
 On 17/09/2012 10:01 PM, tarak karmakar wrote:
 
 Dear All,
 
  I want to have one of tyrosine residues in my protein to
 be unprotonated. I am using amber force field for the simulation. But
 in aminoacid.rtp there is no entry for the unprotonated one. So I am
 adding it by myself in to the .rtp file. Now I am bit confused with
 the charge of the unprotonated one. How can I calculate the partial
 charges for each and every atoms in  unprotonated tyrosine? Would
 Gaussian/SCF be a good one to deal with this matter? Should I take the
 tyrosine amino acid alone to calculate the charge in Gaussian ?
 Please suggest me the proper method(s) to calculate the charge.
 
 
 It varies, but should be determined by the process by which the rest of the
 force field was determined. See
 http://www.gromacs.org/Documentation/How-tos/Parameterization
 
 Mark
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---
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,75124 Uppsala, Sweden
phone:+46 18 471 6688fax: +46 18 511 755
er...@xray.bmc.uu.se
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[gmx-users] DelG of LJ Transformation Negative Glu---Ala Mutation

2012-09-18 Thread Sai Kumar Ramadugu

Hi Gmx Community,
I am doing Glutamate to Alanine mutation in presence and absence of a
ligand.
The Coulomb transformation is yielding the following results:
Glu---Ala + ligand = 790.109 kJ/mol
Glu---Ala + no ligand = 787.33 kJ/mol

During the LJ transformation

Glu---Ala + ligand = - 24.87 kJ/mol
Glu---Ala + no ligand = - 12.4403


The reason I am asking this is because in experiments, the Glu---Ala
mutation yields a positive deldelG but in TI approach, I am getting a
negative deldelG. The major contribution is from the LJ transformation.
With the above values, the deldelG from TI approach is -9.65 kJ/mol

Is it possible to have a negative deldelG for a mutation like Glutamate
(which is charged) to Alanine (which is neutral)?

If it is system dependent and you need more information than what provided
in this email, I will add in happily. But I am just curious to know your
opinions.

Regards
Sai
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Re: [gmx-users] PDB and XYZ Structure Files in GROMACS

2012-09-18 Thread Lara Bunte

Hi Justin

I really forgot this old mail. I am sorry for that. 

editconf worked :)

Greetings
Lara





- Ursprüngliche Message -
Von: Justin Lemkul jalem...@vt.edu
An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users 
gmx-users@gromacs.org
CC: 
Gesendet: 16:04 Dienstag, 18.September 2012
Betreff: Re: [gmx-users] PDB and XYZ Structure Files in GROMACS



On 9/18/12 9:58 AM, Lara Bunte wrote:
 Hello

 Is it possible with GROMACS to convert a given .pdb structure file to a .xyz 
 structure file?


http://gromacs.5086.n6.nabble.com/pdb-to-xyz-file-format-td4998284.html

-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] use of PRODRG

2012-09-18 Thread Elie M


Dear all,
I have been reading about PRODRG that takes a PDB file as an input and produces 
topologies compatible with GROMACS as an output. Can this program be then 
considered as a solution to the problem of missing residues in GROMACS like 
LIG?  
N.B:  I am using the OPLSAA force field .I also have the files in MDL MOL2 
version which do not contain the LIG residue appearing in the PDB file. So 
maybe using PRODRG on the MOL2 might solve the problem?
Regards
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[gmx-users] Extracting bond information from topol.tpr file using template.c

2012-09-18 Thread Amit Shavit

Hello,

I'm relatively new to GROMACS, and I need to write some of my own analysis
tools using the template.c file.
I have been able to figure out most of the structure of it, and how the C
Structs are used. That is to say, I can successfully retrieve particle
positions, residue IDs, residue names, etc.

The one piece of information that I can't seem to be able to retrieve is
bonding information. Is there a way for me to get this? I should mention
that I run the program by inputting a traj.trr and topol.tpr files, so I
have access to the information saved in those files.

Thanks!
Amit
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Re: [gmx-users] Extracting bond information from topol.tpr file using template.c

The topol.top/.itp files have the pairwise bond information.

On 2012-09-18 10:49:25PM -0400, Amit Shavit wrote:
 Hello,
 
 I'm relatively new to GROMACS, and I need to write some of my own analysis
 tools using the template.c file.
 I have been able to figure out most of the structure of it, and how the C
 Structs are used. That is to say, I can successfully retrieve particle
 positions, residue IDs, residue names, etc.
 
 The one piece of information that I can't seem to be able to retrieve is
 bonding information. Is there a way for me to get this? I should mention
 that I run the program by inputting a traj.trr and topol.tpr files, so I
 have access to the information saved in those files.
 
 Thanks!
 Amit
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Re: [gmx-users] Extracting bond information from topol.tpr file using template.c