Re: [gmx-users] ffout

[David van der Spoel]

On 2014-11-16 07:23, Eric Smoll wrote:

Hello Gromacs users,

What is the purpose of the "ffout" flag for mdrun version 4.6.5? It does
not produce output, it appears to have has no impact on my simulations, and
it is not documented in the manual.

Best,
Eric


It's a historic remnant that has been removed in the development code.

--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se
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[gmx-users] Protein comparison

[md kashif]

Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs?

Thanks
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[gmx-users] Building executable for template.c!

[Anjaiah Nalaparaju]

Dear Users,

I want to have executable file for template.c, but not in the default
location and not during the installation of whole package. I am trying to
do this for gromacs-4.6.5.

When I use

$cd /home/user/Documents/

$ tar xfz gromacs-4.6.5.tgz
$ cd gromacs-4.6.5
$ mkdir build
$ cd build
$ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON
-DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON
-DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/

$ make install

It installs gromacs package at /home/user/gromacs4.6.5/ and executable
for template.c is at
/home/user/Documents/gromacs4.6.5/build/share/template/.

What I want to do is, I want to build the executable file for template
not during the installation of whole package.

I have copied the folder "template"distribution directory as
/home/user/Documents/template/. Now I want to build the template using
the already installed gromacs.

I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did
source /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to
build executable I end-up with either of the following error.

-- checking for module 'libgmx_d'
--   package 'libgmx_d' not found
CMake Error at 
/usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
(message):
  Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR)

or

  Could not find a package configuration file provided by "GROMACS" with any
  of the following names:

GROMACSConfig.cmake
gromacs-config.cmake

  Add the installation prefix of "GROMACS" to CMAKE_PREFIX_PATH or set
  "GROMACS_DIR" to a directory containing one of the above files.  If
  "GROMACS" provides a separate development package or SDK, be sure it has
  been installed.

Can anyone please guide me to build the executable for template.c in
the different place using the already installed gromacs package. I
think for the gromacs.4.5 this procedure is bit straight forward

by changing the Makefile we can get it. But for gromacs-4.6.5 seems
not so straight forward.

Thanks in advance for your time and help.
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Re: [gmx-users] Protein comparison

[Onur Tuna]

Dear kashifzamir,

What will you compare? As I guess, if you want to compare the protein structure 
before and after docking, you have to use VMD.

Best
Onur

> On 16 Nov 2014, at 11:43, md kashif  wrote:
> 
> Dear all
> I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
> 
> Thanks
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The information contained in this communication may contain confidential or 
legally privileged information. Hacettepe University doesn't accept any legal 
responsibility for the contents and attachments of this message. The sender 
does not accept any liability for any errors or omissions or any viruses in the 
context of this message which arise as a result of internet transmission.
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Re: [gmx-users] Apply secondary structure restraints only on part of the peptide while coarse graining

[shivangi nangia]

Thanks Tsjerk.
On Nov 12, 2014 3:27 PM, "Tsjerk Wassenaar"  wrote:

> Hi sxn,
>
> You can supply a secondary structure string with the option -ss. That may
> also be provided as a file. you can also just modify the residues you need
> to have different in the dssp output. Only the actual classification string
> is used.
>
> Hope it helps,
>
> Tsjerk
> On Nov 12, 2014 4:00 PM, "shivangi nangia" 
> wrote:
>
> > Hello Dear GMX users,
> >
> > I want to apply secondary structure constraints only on a part of my
> > peptide while coarse graining (martinize.py), which contains a helical
> part
> > and the rest of the structure is disordered.
> >
> > If  I supply a .dssp file only of part of the peptide, I only get the
> first
> > coarse grained part of the peptide back.
> >
> > Is there a way around this?
> >
> > Kindly suggest.
> >
> > Thanks,
> > sxn
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Re: [gmx-users] Flat-bottomed position restraint set

[Oliver Stueker]

Dear Liuyoung,


in your equil.mdp
​ you have ​
:

> ​define  = -D
> ​​
> *​​POSRES​​​*

​​

​and in your topol.top:
​


> #ifdef
> *​​POSRES_WATER*
> ; Position restraint for each water oxygen
> ;[ position_restraints ]
> ;  i funct   fcxfcyfcz
> ;  11   1000   1000   1000
> [ position_restraints ]
> ;  i funct   g r(nm)   k
>121  3.0   30.0
> ;   221  3.0   30.0
> ;   321  3.0   30.0
> #endif


​That means your position_restraints directive will not be included​.

Use whatever word you like for both the define and ifdef line, as long as
it's the same.
e.g. define -DPOSRES  and  #ifdef POSRES
​or define -DPOSRES_FLATBOTTOM and ​#ifdef POSRES_FLATBOTTOM


​Best,
Oliver​



On Sat, Nov 15, 2014 at 11:11 PM, liuyong_1...@dicp.ac.cn <
liuyong_1...@dicp.ac.cn> wrote:

> The content of the equil.mdp and topol.top files is shown as follow.
>
> ​​
> equil.mdp:
>
> title   = NVT Equilibration for Na in 56 water
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 25000 ; 2 * 50,000 = 100 ps ;(100 ns)
> dt  = 0.002 ; 2 fs
> ​​
> define  = -DPOSRES
> ; Output control
> nstxout = 500   ; save coordinates every 0.1 ps
> nstvout = 500   ; save velocities every 1 ps
> nstenergy   = 500   ; save energies every 1 ps
> nstlog  = 500   ; update log file every 1 ps
> nstxtcout= 500
> xtc-precision= 1000
> ; Bond parameters
> continuation= yes   ; Restarting after NVT
> constraint_algorithm = ; holonomic constraints
> constraints =h-angles   ;water both bond and angle constrained
> ;constraints= hbonds; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cels
> nstlist = 1 ; 10 fs
> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
> ; vdw
> vdw-type = Cut-off
> rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field ;cut-off
> rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
> epsilon_rf  = 2.0
> epsilon_r   = 0.5
> cutoff-scheme   = group
> ;pme_order  = 4 ; cubic interpolation
> ;fourierspacing = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> ; annealing = single
> ; annealing_time = 0 40016002400  4000  5600   7200  10400
> 13600  16800 ; 230  260  270  300  330   360
> ; annealing_temp  =0 20  40 6080100120   140
>  160   180 ;  200   220   240   260   280   300
> ; annealing_npoints = 10
> ; Temperature coupling is on
> tcoupl  = nose-hoover ;v-rescale; berendsen; nose-hoover; More
> accurate thermostat
> tc-grps = system ; three coupling groups - more accurate
> tau_t   = 0.1; time constant, in ps
> ref_t   = 547 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl  = no; Pressure coupling on in NPT
> pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
> independent z
> tau_p   = 5.0   ; time constant, in ps
> ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc = no; 3-D PBC
> ; Velocity generation
> gen_vel = no; assign velocities from Maxwell distribution
> gen_temp= 133   ; temperature for Maxwell distribution
> gen_seed= -1; generate a random seed
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the
> solvent/ions
> nstcomm = 1
> comm-mode   = Linear ;ANGULAR;Linear
> comm-grps   =
>
>
>
>
>
>
>
> 
> topol.top :
>
> ;
> ;   File '250_NA_cen.top' was generated
> ;   By user: onbekend (0)
> ;   On host: onbekend
> ;   At date: Tue Aug 12 09:46:55 2014
> ;
> ;   This is a standalone topology file
> ;
> ;   It was generated using program:
> ;   pdb2gmx_d - VERSION 4.5.5
> ;
> ;   Command line was:
> ;   pdb2gmx_d -f water250_NA_cen.pdb -p 250_NA_cen.top -o 250_NA_cen.gro
> ;
> ;   Force field was read from the standard Gromacs share directory.
> ;
>
> ; Include forcefield parameters
> #include "amber94.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Namenrexcl
> Ion 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
> ; residue   1 NA  rtp NA   q +1.0
>  1 Na  1 NA NA  1  1  22.99   ;
> qtot 

[gmx-users] Umbrella Sampling and flat-bottom position restraints

[Oliver Stueker]

Dear fellow Gromacs Users,

I'm trying to calculate the binding free energy between a protein and a
small molecule using Umbrella Sampling.

I made my first attempt last year using Gromacs 4.5 and ran into the same
convergence problems that have been pointed out on the mailing list several
times.
To overcome these problems I now want to give it another try utilizing the
flat-bottomed position restraints that have been introduced in Gromacs 5.0.

My plan is to perform the Umbrella sampling along the Z-axis and to
restrict the protein as well as the ligand with flat-bottomed position
restraints along X and Y into a cylindrical space (as suggested e.g. by
Chris Neale in [1]).

But I'm not quite sure what radius the cylinder should have ( or how wide
the flat bottom should be).
The protein is roughly spherical with a diameter of ~4nm. I was initially
thinking to use an r_{fb} of 2nm for the protein and  for the ligand 1/2 of
it's longest dimension to allow both of them to re-orient freely. But the
more I think about, I'm afraid that it's too large.

Has anyone have experience with that? Maybe even a published paper?
So far I've unsuccessfully tried several times to find a published method.


Also to I need to consider the flat-bottomed potential when doing the
g_wham analysis?


Thanks,
Oliver


[1]
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/087644.html
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Re: [gmx-users] Tryptophan Hbond Bug

[Justin Lemkul]

On 11/15/14 7:24 PM, Alexander Law wrote:

I may have found a bug in the vmx hbond command. In short the cyclic nitrogen
within the indole ring on a tryptophan side chain is behaving as both Hbond
acceptor and donor. The end result of this is a constant Hbond being show in
the output .xvg. Here are some of the detail which led me to this conclusion,
it must be said however I am a novice and am most likely doing something
wrong, regardless there is a problem. note: -nitacc did nothing.

I am looking at a potential hydrogen bond forming between the side chain
carboxyl group on an aspartate and the cyclic nitrogen in the tryptophan
indole ring. At first my index groups were the whole residues, but I found
this produced too many Hbond using the -dan command, I then cut it down to
the aspartate carboxyl oxygens (2 atoms) and the tryptophan nitrogen and the
studied hydrogen (2 atoms). This gave 1 continuos Hbond forming across the
whole 200ns simulation. This is false result, viewing this interaction in VMD
showed the aspartate fluctuating outside reasonable Hbond distance. These 2
index groups gave 3 acceptors and 1 donor. 2 of the acceptors are the
aspartate oxygens, I assumed the donor is the nitrogen but the 3rd acceptor?
I then used the tryptophan N-H and just the N, this gave 2 acceptors and 1
donor, using N-H and just the H gave 1 acceptor and 1 donor. Trying to avoid
the nitrogen altogether I used the asp 2 oxygen atoms and just the hydrogen
atom from the N-H in tryptophan only gave two acceptors. I am at a loss...
any advise, questions to investigate more or answers are appreciated!



All of this seems consistent with what gmx hbond should be doing.  So revisit 
the original premise and quantify what's going on - your only evidence thus far 
that there should not be a hydrogen bond is via VMD.  What does g_dist tell you 
about the distances between these atoms?  Can you show conclusively that the 
distances are outside what can be considered a hydrogen bond?  Are there any 
other anomalous pairs that reproduce the issue?  There is no reason to think 
that there is a "tryptophan bug," as the calculations are the same, irrespective 
of molecular identity.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Understanding Force Plot in Umbrella Sampling Simulations

[Justin Lemkul]

On 11/15/14 9:48 PM, Agnivo Gosai wrote:

Dear Users

I have been following the Umbrella Sampling simulation by Dr. Lemkul and
applying the concepts for my project.

After reading Dr. Lemkul's paper associated with the tutorial , I
understand that the Force vs Time plots will have different peaks and
slopes , but similar profiles , in the Steered Molecular Dynamics case. It
will vary with different pull rates and force constants. After that a
series of sampling configurations are extracted to do the Umbrella Sampling
simulations. Here the pull rate is 0. But this also generates Force vs Time
plots. And through the WHAM algorithm we can find the PMF versus the pulled
distance ( reaction coordinate ).

Now I want to quantify the binding force between molecules A and B. From
SMD I have a F vs t plot. From different samples I have different F vs t
plots. (23 in my case ). Also I think if I take the derivative of the PMF
with respect to the reaction coordinate , I shall have a F vs x plot.



Just plot the actual distances from g_dist or the pullx.xvg output.


But I am not sure as to how to analyze the data and pin point a range for
the "binding force " between the 2 molecules.
Hence my questions are :- (1) Should I look at the F vs x plot generated
from the PMF profile ?



What is a "binding force," exactly?


(2) What inference should I draw from the intial F vs t plots from the SMD
part.



The path along which the system evolves under the imposed bias.


(3) What to do with the different F vs t plots from the sampling
simulations ? The pullf and pullx are input to the WHAM algorithm but can I
draw inferences from the individual plots ?



Not much.  During US, the F vs. t is just the magnitude of force applied to 
restore the restrained degree of freedom to its target value.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Protein comparison

[Justin Lemkul]

On 11/16/14 4:43 AM, md kashif wrote:

Dear all
  I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs?



Gromacs is used to perform simulations.  So you need to define what "compare" 
means in terms of something that can be observed using a dynamical simulation.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Umbrella Sampling and flat-bottom position restraints

[Justin Lemkul]

On 11/16/14 1:04 PM, Oliver Stueker wrote:

Dear fellow Gromacs Users,

I'm trying to calculate the binding free energy between a protein and a
small molecule using Umbrella Sampling.

I made my first attempt last year using Gromacs 4.5 and ran into the same
convergence problems that have been pointed out on the mailing list several
times.
To overcome these problems I now want to give it another try utilizing the
flat-bottomed position restraints that have been introduced in Gromacs 5.0.

My plan is to perform the Umbrella sampling along the Z-axis and to
restrict the protein as well as the ligand with flat-bottomed position
restraints along X and Y into a cylindrical space (as suggested e.g. by
Chris Neale in [1]).

But I'm not quite sure what radius the cylinder should have ( or how wide
the flat bottom should be).
The protein is roughly spherical with a diameter of ~4nm. I was initially
thinking to use an r_{fb} of 2nm for the protein and  for the ligand 1/2 of
it's longest dimension to allow both of them to re-orient freely. But the
more I think about, I'm afraid that it's too large.



Why is it necessary to pull only along the z-axis?  For simple ligand binding to 
a globular protein, you can define the pull vector in any or all of the three 
spatial dimensions.  Is there some reason you presuppose binding only along z?



Has anyone have experience with that? Maybe even a published paper?
So far I've unsuccessfully tried several times to find a published method.


Also to I need to consider the flat-bottomed potential when doing the
g_wham analysis?



It's an additional bias to the Hamiltonian, so it should probably be accounted 
for in some way.  As to how, I'm not sure.  But it's an additional degree of 
freedom that is being restrained.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Building executable for template.c!

[Mark Abraham]

On Sun, Nov 16, 2014 at 1:06 PM, Anjaiah Nalaparaju 
wrote:

> Dear Users,
>
> I want to have executable file for template.c, but not in the default
> location and not during the installation of whole package. I am trying to
> do this for gromacs-4.6.5.
>
> When I use
>
> $cd /home/user/Documents/
>
> $ tar xfz gromacs-4.6.5.tgz
> $ cd gromacs-4.6.5
> $ mkdir build
> $ cd build
> $ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON
> -DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON
> -DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/
>
> $ make install
>
> It installs gromacs package at /home/user/gromacs4.6.5/ and executable
> for template.c is at
> /home/user/Documents/gromacs4.6.5/build/share/template/.
>
> What I want to do is, I want to build the executable file for template
> not during the installation of whole package.
>

That's good, because you can't do the alternative. The template is designed
for use from the installation...


> I have copied the folder "template"distribution directory as
> /home/user/Documents/template/. Now I want to build the template using
> the already installed gromacs.
>
> I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did
> source /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to
> build executable I end-up with either of the following error.
>

... so don't do this, get your stuff from
/where/you/installed/share/gromacs/template where (e.g.) that renaming (and
any interpolation required) are already handled (though IIRC there's none
of the latter for 4.6).


> -- checking for module 'libgmx_d'
> --   package 'libgmx_d' not found
> CMake Error at
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108
> (message):
>   Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR)
>
> or
>
>   Could not find a package configuration file provided by "GROMACS" with
> any
>   of the following names:
>
> GROMACSConfig.cmake
> gromacs-config.cmake
>
>   Add the installation prefix of "GROMACS" to CMAKE_PREFIX_PATH or set
>   "GROMACS_DIR" to a directory containing one of the above files.  If
>   "GROMACS" provides a separate development package or SDK, be sure it has
>   been installed.
>
> Can anyone please guide me to build the executable for template.c in
> the different place using the already installed gromacs package. I
> think for the gromacs.4.5 this procedure is bit straight forward
>
> by changing the Makefile we can get it. But for gromacs-4.6.5 seems
> not so straight forward.
>

There's a README in the template folder that suggests you source GMXRC.
IIRC the template depends on pkg-config and source GMXRC is the main way to
make that work.

Mark

Thanks in advance for your time and help.
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[gmx-users] fitting problem

[Rohit Farmer]

Hi there,

I am trying to fit a protein to a reference structure using the command
below

trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive

I am using protein for least square and system for output.

This command always worked for me but for this particular protein the side
chains get crooked. I don't know how to explain but they look like flat
structures with random bonds between the atoms.

I tried -pbc mol and whole instead of fit just to get rid of the pbc effect
and don't care about fitting. But it also gave the same result.

Can someone please help.

Thanks

Rohit
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Re: [gmx-users] fitting problem

[Mark Abraham]

On Sun, Nov 16, 2014 at 9:08 PM, Rohit Farmer 
wrote:

> Hi there,
>
> I am trying to fit a protein to a reference structure using the command
> below
>
> trjconv -s run.trp -f run.xtc -o run-fit.xtc -fit progressive
>

Please copy and paste your actual command. Not what you think it was +
typos + whatever changes you don't think matter :-).


>
> I am using protein for least square and system for output.
>
> This command always worked for me but for this particular protein the side
> chains get crooked. I don't know how to explain but they look like flat
> structures with random bonds between the atoms.
>

So take a screenshot, upload to a file-sharing service and share the link.


> I tried -pbc mol and whole instead of fit just to get rid of the pbc effect
> and don't care about fitting. But it also gave the same result.
>

Then you may be trying to fit files whose topology atom ordering does not
match, or something like that. Note that if the molecules aren't whole in
the .tpr file, then you won't be doing anything useful with some of the
-pbc options.

Mark


> Can someone please help.
>
> Thanks
>
> Rohit
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Re: [gmx-users] Umbrella Sampling and flat-bottom position restraints

[Oliver Stueker]

Hi Justin,

Thanks for the feedback.

On Sun, Nov 16, 2014 at 2:51 PM, Justin Lemkul  wrote:

>
>
> On 11/16/14 1:04 PM, Oliver Stueker wrote:
>
>> Dear fellow Gromacs Users,
>>
>> I'm trying to calculate the binding free energy between a protein and a
>> small molecule using Umbrella Sampling.
>>
>> I made my first attempt last year using Gromacs 4.5 and ran into the same
>> convergence problems that have been pointed out on the mailing list
>> several
>> times.
>> To overcome these problems I now want to give it another try utilizing the
>> flat-bottomed position restraints that have been introduced in Gromacs
>> 5.0.
>>
>> My plan is to perform the Umbrella sampling along the Z-axis and to
>> restrict the protein as well as the ligand with flat-bottomed position
>> restraints along X and Y into a cylindrical space (as suggested e.g. by
>> Chris Neale in [1]).
>>
>> But I'm not quite sure what radius the cylinder should have ( or how wide
>> the flat bottom should be).
>> The protein is roughly spherical with a diameter of ~4nm. I was initially
>> thinking to use an r_{fb} of 2nm for the protein and  for the ligand 1/2
>> of
>> it's longest dimension to allow both of them to re-orient freely. But the
>> more I think about, I'm afraid that it's too large.
>>
>>
> Why is it necessary to pull only along the z-axis?  For simple ligand
> binding to a globular protein, you can define the pull vector in any or all
> of the three spatial dimensions.  Is there some reason you presuppose
> binding only along z?
>

​Hmm, indeed it's probably not necessary to ​pull only along Z. However the
box would need to be much larger if I can't control the direction.
In my first attempt I had already aligned the vector between the COMs of
Protein and ligand with the Z-axis so that I can pull along that direction.
That time I've used a box of 10 x 10 x 15 nm.

Last time I've used the following pull settings:
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

​I also had the problem that during the equillibration of the Umbrella
windows the ligand ​moved a bit away from it's initial position so that the
initial pull distance was a bit off. This time I want to prevent that by
setting pull_init for each window directly and leave pull_start = off.

​Say if I ​use pull_dim = Y Y Y and a cubic box of 15 x 15 x 15 nm. That
would restrict the ligand to the surface of a sphere of radius d (COM
reference distance of the umbrella window) around the protein. Wouldn't
that mean that I would need to sample the ligand conformations on the
complete surface of each sphere to achieve sufficient conformational
overlap between neighbouring windows? Those surfaces would become quite big
once I reach to high COM distances (6 nm).
Say if in two windows n-1 and n+1 the ligand moves towards +X / +Y and in
window n (in between) the ligand moves to -X / -Y. Then while the
histograms might overlap nicely (according the sampled COM distances) the
sampled conformations might be very different.

​It seems that simply using pull_dim = Y Y Y would also not really solve
the problem.​



>  Has anyone have experience with that? Maybe even a published paper?
>> So far I've unsuccessfully tried several times to find a published method.
>>
>>
>> Also to I need to consider the flat-bottomed potential when doing the
>> g_wham analysis?
>>
>>
> It's an additional bias to the Hamiltonian, so it should probably be
> accounted for in some way.  As to how, I'm not sure.  But it's an
> additional degree of freedom that is being restrained.
>

​Yes, you are probably right.

Would this work:

   - generate conformations by pulling along Z and select conformations for
   windows
   - equillibrate each window
   - run umbrella-sampling (to sample conformations/coordinates) along Z
   with pull_init = d(window) and use flat-bottomed PosRes to restrict Protein
   and Ligand in X/Y movement.
  - as reference coordinates, I use the COM of Protein and ligand
  respectively
  - as r_{fb} I can use the radius of the sphere that encloses the
  protein (or ligand) plus a small buffer.
  - store coordinates in XTC and discard the pullx- / pullf- files.
   - Do a re-run umbrella-sampling (to generate distances/forces) with pull_dim
   = Y Y Y and without the PosRes to generate the pullx / pullf files that
   will be used for g_wham.

​Instead of the last re-run I could maybe also run g_dist to generate my
pullx.xvg files and then pass g_wham tpr files with pull_dim = Y Y Y and
without the PosRes.


Best,
Oliver



> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of

[gmx-users] problem with phosphorylated serine

[Jayant James]

Hi !
I downloaded the ffG43a1p.tar.gz
 for
simulations of phosphorylated serines (downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
error (below). Well there is no "HISE" in the input pdb file. There is a
SEP. So I thought I'd better get help from the GMX community. I also found
that if I were to execute a pdb file without any phosphorylated serine the
pdb2gmx runs all the way to the end and the gives the error message similar
to one below.

Error message


"Program pdb2gmx, VERSION 4.5.4
Source code file: resall.c, line: 581
Fatal error:
Residue 'HISE' not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors";
Thanks!
JJ
PS.

I execute a modular command to enable execution of GMX from my directory
the commands are below
setenv GROMACSHOME /share/apps/gromacs/4.5.4/single
prepend-path PATH /share/apps/gromacs/4.5.4/single/bin
prepend-path LD_LIBRARY_PATH /share/apps/gromacs/4.5.4/single/lib
prepend-path MANPATH /share/apps/gromacs/4.5.4/single/man




http://www.chick.com/reading/tracts/0076/0076_01.asp
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Re: [gmx-users] Flat-bottomed position restraint set

[liuyong_1...@dicp.ac.cn]

Dear Oliver​,

From you explaination, I modify the equil.mdp file as
   define = -DPOSRES_WATER

and the topol.top file as :

; Include forcefield parameters
#include "amber94.ff/forcefield.itp"

[ moleculetype ]
; Namenrexcl
Ion 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
; residue   1 NA  rtp NA   q +1.0
 1 Na  1 NA NA  1  1  22.99   ; qtot 1

; Include topology for ions
#include "amber94.ff/ions.itp"

#ifdef POSRES_ion
[ position_restraints ]
;  i funct   g r(nm)   k
;   121  3.0   30.0
#endif


; Include water topology
#include "amber94.ff/spce.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   g r(nm)   k
   121  3.0   30.0
;   221  3.0   30.0
;   321  3.0   30.0
#endif

Dose it means that the position restraints are applied to all the oxyen atoms 
of  the water molecules ?

Best regards,
Yong Liu



liuyong_1...@dicp.ac.cn

From: Oliver Stueker
Date: 2014-11-17 00:46
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Flat-bottomed position restraint set
Dear Liuyoung,


in your equil.mdp
​ you have ​
:

> ​define  = -D
> ​​
> *​​POSRES​​​*

​​

​and in your topol.top:
​


> #ifdef
> *​​POSRES_WATER*
> ; Position restraint for each water oxygen
> ;[ position_restraints ]
> ;  i funct   fcxfcyfcz
> ;  11   1000   1000   1000
> [ position_restraints ]
> ;  i funct   g r(nm)   k
>121  3.0   30.0
> ;   221  3.0   30.0
> ;   321  3.0   30.0
> #endif


​That means your position_restraints directive will not be included​.

Use whatever word you like for both the define and ifdef line, as long as
it's the same.
e.g. define -DPOSRES  and  #ifdef POSRES
​or define -DPOSRES_FLATBOTTOM and ​#ifdef POSRES_FLATBOTTOM


​Best,
Oliver​



On Sat, Nov 15, 2014 at 11:11 PM, liuyong_1...@dicp.ac.cn <
liuyong_1...@dicp.ac.cn> wrote:

> The content of the equil.mdp and topol.top files is shown as follow.
>
> ​​
> equil.mdp:
>
> title   = NVT Equilibration for Na in 56 water
> ; Run parameters
> integrator  = md; leap-frog integrator
> nsteps  = 25000 ; 2 * 50,000 = 100 ps ;(100 ns)
> dt  = 0.002 ; 2 fs
> ​​
> define  = -DPOSRES
> ; Output control
> nstxout = 500   ; save coordinates every 0.1 ps
> nstvout = 500   ; save velocities every 1 ps
> nstenergy   = 500   ; save energies every 1 ps
> nstlog  = 500   ; update log file every 1 ps
> nstxtcout= 500
> xtc-precision= 1000
> ; Bond parameters
> continuation= yes   ; Restarting after NVT
> constraint_algorithm = ; holonomic constraints
> constraints =h-angles   ;water both bond and angle constrained
> ;constraints= hbonds; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter  = 1 ; accuracy of LINCS
> lincs_order = 4 ; also related to accuracy
> ; Neighborsearching
> ns_type = grid  ; search neighboring grid cels
> nstlist = 1 ; 10 fs
> rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
> ; vdw
> vdw-type = Cut-off
> rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
> ; Electrostatics
> coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field ;cut-off
> rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
> epsilon_rf  = 2.0
> epsilon_r   = 0.5
> cutoff-scheme   = group
> ;pme_order  = 4 ; cubic interpolation
> ;fourierspacing = 0.16  ; grid spacing for FFT
> ; Temperature coupling is on
> ; annealing = single
> ; annealing_time = 0 40016002400  4000  5600   7200  10400
> 13600  16800 ; 230  260  270  300  330   360
> ; annealing_temp  =0 20  40 6080100120   140
>  160   180 ;  200   220   240   260   280   300
> ; annealing_npoints = 10
> ; Temperature coupling is on
> tcoupl  = nose-hoover ;v-rescale; berendsen; nose-hoover; More
> accurate thermostat
> tc-grps = system ; three coupling groups - more accurate
> tau_t   = 0.1; time constant, in ps
> ref_t   = 547 ; reference temperature, one for each group, in K
> ; Pressure coupling is on
> pcoupl  = no; Pressure coupling on in NPT
> pcoupltype  = semiisotropic ; uniform scaling of x-y box vectors,
> independent z
> tau_p   = 5.0   ; time constant, in ps
> ref_p   = 1.0   1.0 ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-54.5e-5  ; isothermal compressibility, bar^-1
> ; Periodic boundary conditions
> pbc = no; 3-D PBC
> ; Velocit

Re: [gmx-users] Building executable for template.c!

[Anjaiah Nalaparaju]

I used Makefile instead of cmake. It is working now and I can build the
executable as required.


Thanks.

On Sun, Nov 16, 2014 at 8:06 PM, Anjaiah Nalaparaju 
wrote:

> Dear Users,
>
> I want to have executable file for template.c, but not in the default
> location and not during the installation of whole package. I am trying to
> do this for gromacs-4.6.5.
>
> When I use
>
> $cd /home/user/Documents/
>
> $ tar xfz gromacs-4.6.5.tgz
> $ cd gromacs-4.6.5
> $ mkdir build
> $ cd build
> $ cmake .. -DGMX_MPI=ON -DGMX_GPU=OFF -DGMX_BUILD_OWN_FFTW=ON 
> -DGMX_DEFAULT_SUFFIX=ON -DGMX_DOUBLE=ON 
> -DCMAKE_INSTALL_PREFIX=/home/user/gromacs4.6.5/
>
> $ make install
>
> It installs gromacs package at /home/user/gromacs4.6.5/ and executable for 
> template.c is at /home/user/Documents/gromacs4.6.5/build/share/template/.
>
> What I want to do is, I want to build the executable file for template not 
> during the installation of whole package.
>
> I have copied the folder "template"distribution directory as 
> /home/user/Documents/template/. Now I want to build the template using the 
> already installed gromacs.
>
> I have renamed the CMakeLists.txt.template to CMakeLists.txt. Then did source 
> /home/user/gromacs4.6.5/bin/GMXRC.bash. When I used cmake to build executable 
> I end-up with either of the following error.
>
> -- checking for module 'libgmx_d'
> --   package 'libgmx_d' not found
> CMake Error at 
> /usr/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:108 
> (message):
>   Could NOT find GROMACS (missing: GROMACS_LIBRARY GROMACS_INCLUDE_DIR)
>
> or
>
>   Could not find a package configuration file provided by "GROMACS" with any
>   of the following names:
>
> GROMACSConfig.cmake
> gromacs-config.cmake
>
>   Add the installation prefix of "GROMACS" to CMAKE_PREFIX_PATH or set
>   "GROMACS_DIR" to a directory containing one of the above files.  If
>   "GROMACS" provides a separate development package or SDK, be sure it has
>   been installed.
>
> Can anyone please guide me to build the executable for template.c in the 
> different place using the already installed gromacs package. I think for the 
> gromacs.4.5 this procedure is bit straight forward
>
> by changing the Makefile we can get it. But for gromacs-4.6.5 seems not so 
> straight forward.
>
> Thanks in advance for your time and help.
>
>
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Re: [gmx-users] Protein comparison

[md kashif]

Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs? With the word "compare "
I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change? Kindly
suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
>
> Thanks
>
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