date:20180516

Re: [gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Naba

>
> On 5/16/18 3:32 AM, Naba wrote:
> > Dear all,
> >
> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> > acids from its homodimer in opposite directions along z axis. The
> > interfaces of each protein chain is parallel to the z axis. I do not need
> > any restraints in this case. I have gone through the GROMACS manual and
> > some of the previous archived messages and set the following mdp options.
> >
> > ; Pull code
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 2
> > pull_group1_name= chain_A
> > pull_group2_name= chain_B
> > ;pull_group3_name = Protein
> > pull_coord1_type = umbrella
> > pull_coord2_type = umbrella
> > pull_coord1_init = 0.0
> > pull_coord2_init = 0.0
> > pull_coord1_start = yes   ; define initial COM distance > 0
> > pull_coord2_start = yes
> > pull_coord1_geometry= direction
> > pull_coord2_geometry= direction
> > pull_coord1_groups  = 2 1
> > pull_coord2_groups  = 1 2
> > pull_coord1_dim = N N Y
> > pull_coord2_dim = N N Y
>
> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>
> > pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
> > pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
> > pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> > pull_coord2_k   = 2000
> > pull_coord1_vec= 0.0 0.0 1.0
> > pull_coord2_vec= 0.0 0.0 -1.0
> > nstcalcenergy = 1
> > nhchainlength = 1
> >
> > But it fails to pull chain_A in positive z direction. However, chain_B is
> > seemed to pull in negative z direction. Someone please suggest the proper
> > way to pull two groups in opposite directions, or if there is anything
> that
> > I am missing.
>
> What is the point of pulling in two directions? Separation of two
> species requires only one reaction coordinate. For every action, there
> is an equal, but opposite reaction...
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==



Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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[gmx-users] Protein protein complex simulation to be done with respect to observe changes in temperature

2018-05-16 Thread SHYANTANI MAITI

Dear all,
Do we need to change any other parameters other than ref_t and gen_temp
should be changed if I want to perform protein protein complex md
simulation at different temperatures of the same input protein. Is it
necessary to equilibrate the average pressure value to 1 bar before running
the final md simulation?

Thanks in advance,

-- 
Best regards,
*Shyantani Maiti*
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[gmx-users] partial exclusion of interactions within 1-4

2018-05-16 Thread Alex

Hi all,

I think I understand how it works, but to double-check... There's a paper
describing a setup of intramolecular interactions for boron nitride (
https://pubs.acs.org/doi/10.1021/acs.jpclett.7b03443), in which non-bonded
interactions *within* 1-4 were set up in the following way: LJ is off, but
all electrostatic interactions are on. This is to achieve a better
representation of the phonon spectrum and in fact it appears physically
correct.

Does this mean setting nrexcl to 1 for the crystal topology and creating a
table of nonbond_param between B and N with sigma and epsilon equal to 0?

Thanks,

Alex
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Re: [gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Justin Lemkul




On 5/16/18 3:32 AM, Naba wrote:

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y


Note that pull_coord*_dim is not relevant when using "direction" geometry.


pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.


What is the point of pulling in two directions? Separation of two 
species requires only one reaction coordinate. For every action, there 
is an equal, but opposite reaction...


-Justin

--
==

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com

==

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Re: [gmx-users] C6-C12 table potential

2018-05-16 Thread Alex

Hi,
Thanks.

On Wed, May 16, 2018 at 3:09 PM, Mark Abraham 
wrote:

> Hi,
>
> I would assume not, because it's more useful to be able to let a user
> specify a table for an energy group and for that to contain different atom
> types.
>
I'm afraid I did get your point!
What I know is that the potential V(r) = 1/r + C12/(r^12) - C6/(r^6) and
then force F(r) = -dV/dr = 1/(r2) + 12*C12/(r^13) - 6*C6/(r^7) which all
together would make the table_A_B.xvg with 7 columns.
In Gromacs the unit of \sigma and \epsilon in C12 = 4*\epsilon*\sigma^12
and C6 = 4*\epsilon*\sigma^6 are nm and kj/mol, do you know if the C12 and
C6 reported in the Martini FF are using the same unit?

>
> But your best friend is to test both your understanding and the code by
> e.g. making a structure file with two such atoms 1nm apart and observing
> what force you get from a suitable mdrun -rerun with various tables.
>
 With various tables, do you mean playing around with the C6 and C12? How
much I should differ the C6 and C12 respect to the above numerical
parameters.

BTW, I am going to use this table as the initial guess for in a IBI
coarse-grained parametrisation.

Thank you and regards,
Alex

>
> Mark
>
> On Wed, May 16, 2018 at 8:59 PM Alex  wrote:
>
> > Hi,
> > Suppose that the C6 and C12 for the nonbonded interaction between two
> beads
> > of P4 and SNa in the Martini force fields are as following:
> > C6   C12
> > P4SNda1   0.17246E-00 0.18590E-02 ; semi attractive
> >
> > Now, I was wondering how I can generate a table potential
> > (table_P4_SNda.xvg) using the above C6 and C12 parameters?
> >
> > I guess the general below C code provided in the gromacs tabulated
> > potential does the job, but I am not sure if the columns of -1/r6(-1/r7)
> > and 1/r12(1/r13) should be multiplied by the above C6 and C12
> parameters!?
> >
> > #include 
> > #include 
> >
> > main()
> > {
> > FILE*fout;
> > double  r;
> >
> > fout = fopen("table_example.xvg", "w");
> > fprintf(fout, "#\n# Example LJ 6-12 Potential\n#\n");
> >
> > for (r=0; r<=2.4; r+=0.002) {
> >
> > double f = 1/r;
> > double fprime = 1/(pow(r,2));
> >
> > double g = -1/(pow(r,6));
> > /*   *C6   ? */
> > double gprime = -6/(pow(r,7));/*
> > *C6   ? */
> >
> > double h = 1/(pow(r,12));
> > /*   *C12   ? */
> > double hprime = 12/(pow(r,13)); /*
> > *C12   ? */
> >
> > /* print output */
> > if (r<0.001) {
> > fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
> > %12.10e %12.10e\n", r,0.0,0.0,0.0,0.0,0.0,0.0);
> > } else {
> > fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
> > %12.10e %12.10e\n", r,f,fprime,g,gprime,h,hprime);
> > }
> > }
> >
> > fclose(fout);
> > return(0);
> > }
> >
> > Regards,
> > Alex
> > --
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> >
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Re: [gmx-users] C6-C12 table potential

2018-05-16 Thread Mark Abraham

Hi,

I would assume not, because it's more useful to be able to let a user
specify a table for an energy group and for that to contain different atom
types.

But your best friend is to test both your understanding and the code by
e.g. making a structure file with two such atoms 1nm apart and observing
what force you get from a suitable mdrun -rerun with various tables.

Mark

On Wed, May 16, 2018 at 8:59 PM Alex  wrote:

> Hi,
> Suppose that the C6 and C12 for the nonbonded interaction between two beads
> of P4 and SNa in the Martini force fields are as following:
> C6   C12
> P4SNda1   0.17246E-00 0.18590E-02 ; semi attractive
>
> Now, I was wondering how I can generate a table potential
> (table_P4_SNda.xvg) using the above C6 and C12 parameters?
>
> I guess the general below C code provided in the gromacs tabulated
> potential does the job, but I am not sure if the columns of -1/r6(-1/r7)
> and 1/r12(1/r13) should be multiplied by the above C6 and C12 parameters!?
>
> #include 
> #include 
>
> main()
> {
> FILE*fout;
> double  r;
>
> fout = fopen("table_example.xvg", "w");
> fprintf(fout, "#\n# Example LJ 6-12 Potential\n#\n");
>
> for (r=0; r<=2.4; r+=0.002) {
>
> double f = 1/r;
> double fprime = 1/(pow(r,2));
>
> double g = -1/(pow(r,6));
> /*   *C6   ? */
> double gprime = -6/(pow(r,7));/*
> *C6   ? */
>
> double h = 1/(pow(r,12));
> /*   *C12   ? */
> double hprime = 12/(pow(r,13)); /*
> *C12   ? */
>
> /* print output */
> if (r<0.001) {
> fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
> %12.10e %12.10e\n", r,0.0,0.0,0.0,0.0,0.0,0.0);
> } else {
> fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
> %12.10e %12.10e\n", r,f,fprime,g,gprime,h,hprime);
> }
> }
>
> fclose(fout);
> return(0);
> }
>
> Regards,
> Alex
> --
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[gmx-users] C6-C12 table potential

2018-05-16 Thread Alex

Hi,
Suppose that the C6 and C12 for the nonbonded interaction between two beads
of P4 and SNa in the Martini force fields are as following:
C6   C12
P4SNda1   0.17246E-00 0.18590E-02 ; semi attractive

Now, I was wondering how I can generate a table potential
(table_P4_SNda.xvg) using the above C6 and C12 parameters?

I guess the general below C code provided in the gromacs tabulated
potential does the job, but I am not sure if the columns of -1/r6(-1/r7)
and 1/r12(1/r13) should be multiplied by the above C6 and C12 parameters!?

#include 
#include 

main()
{
FILE*fout;
double  r;

fout = fopen("table_example.xvg", "w");
fprintf(fout, "#\n# Example LJ 6-12 Potential\n#\n");

for (r=0; r<=2.4; r+=0.002) {

double f = 1/r;
double fprime = 1/(pow(r,2));

double g = -1/(pow(r,6));
/*   *C6   ? */
double gprime = -6/(pow(r,7));/*
*C6   ? */

double h = 1/(pow(r,12));
/*   *C12   ? */
double hprime = 12/(pow(r,13)); /*
*C12   ? */

/* print output */
if (r<0.001) {
fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
%12.10e %12.10e\n", r,0.0,0.0,0.0,0.0,0.0,0.0);
} else {
fprintf(fout, "%12.10e   %12.10e %12.10e   %12.10e %12.10e
%12.10e %12.10e\n", r,f,fprime,g,gprime,h,hprime);
}
}

fclose(fout);
return(0);
}

Regards,
Alex
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[gmx-users] Topology file

2018-05-16 Thread Salman Zarrini

Dear all,
I want to create a topol.top file for Silica slab for which the force
fields parameters are available in literature as well as in the lammps.data
file which works fine in lammps (below links). The slab has in general 2184
atom including two types of O atom(OS in surface part and OB in the bulk
part), one Si type and one hydrogen type HS. The gro file can be found in
the below link.

*.gro file*
https://drive.google.com/open?id=1BMdNcqaSIxkMMr89VzUmrIGQOZlusaG0

*lammps.data file*
https://drive.google.com/open?id=1Aqpyv4Mc3VEZGGYaxEuOpbdizVpbs5xR

Would you please help me set up the topol.top file for such system?

For starting, I have prepared the the below topol.top file by considering
the unit conversion and and other cures, however I do not know where I am
doing wrong that causes mismatching between some atoms in gro file and in
topol file as the first error.

One possible approach might be to include all the atoms, bonds and angles
directly in the [ atom ], [ bonds ] and [ angles ] sections of topol.top,
respectively, but that would be so frustrating.

;%*  topol.top* %%

#include "gromos54a7.ff/forcefield.itp"

[ atomtypes ]
;   name  masschargeptype
sigma  epsilon
OB   15.999400-0.550A
0.30914185519469770 0.226087102152
OS   15.999400-0.675A
0.30914185519469770 0.510789378936
Si 28.086000+1.100   A
0.36972296802824080 0.389372231484
HS1.008+0.400   A
0.09666251091822681 0.062801972820

[ moleculetype ]
; molname   nrexcl
GF 3

[ atoms ]
;id at_typeres_nr  residu_nameat_name cgnr  charge
1 OB  1   GFOB 1   -0.550
15.999400
2 OS  1   GFOS 1   -0.675
15.999400
3 Si1   GFSi   1   +1.100
28.086000
4 HS   1   GFHS 1   +0.400
1.008

[ bonds ]
; i j   funct   length  force.c.
1   3   1   0.16800  238647.4967162 ;;OB-Si
2   3   1   0.16800  238647.4967160 ;;OS-Si
2   4   1   0.09450  414493.0206116 ;;OS-HS

[ angles ]
; i j   k   funct   angle  force.c.
2   3   1   1   109.500  837.3596376;; OS-Si-OB
1   3   1   1   109.500  837.3596376;; OB-Si-OB
3   1   3   1   149.000  837.3596376;; Si-OB-Si
3   2   4   1   115.000  418.6798188;; Si-OS-HS

[ system ]
; Name
GF

[ molecules ]
GF   546 ;;; 546*4 = 2184 atoms in gro file

;%%%

Thank you.
Salman
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Re: [gmx-users] secondary structure analysis

2018-05-16 Thread Joe Jordan

You may want to familiarize yourself with how the terminal works before
proceeding. You need to give the path on your machine for dssp.

On Wed, May 16, 2018 at 12:13 PM, SHAHEE ISLAM 
wrote:

> when i am using command
> dssp -h
> below are shown on the terminal screen
> DSSP 2.0.4 options:
>   -h [ --help ] Display help message
>   -i [ --input ] argInput file
>   -o [ --output ] arg   Output file, use 'stdout' to output to screen
>   -v [ --verbose ]  Verbose output
>   --version Print version
>   -d [ --debug ] argDebug level (for even more verbose output)
>
>
> Examples:
>
> To calculate the secondary structure for the file 1crn.pdb and
> write the result to a file called 1crn.dssp, you type:
>
>   dssp.exe -i 1crn.pdb -o 1crn.dssp
>
> but when i am trying
> dssp.exe -i 5B1F2.PDB -o 1crn.dssp
> error is
> dssp.exe: command not found
> thanking you
>
> On 5/16/18, Joe Jordan  wrote:
> > Have you tried running the dssp command on a pdb file to ensure that it
> is
> > working as intended? FYI 4.5.5 is no longer supported so you may want to
> > consider upgrading to (the much faster) gromacs 2018.
> >
> > On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM 
> > wrote:
> >
> >> i have installed dssp2.04 in usr/local/bin.
> >>
> >> On 5/16/18, Joe Jordan  wrote:
> >> > You have to point to where you have dssp installed. This may require
> >> > you
> >> to
> >> > install dssp.
> >> >
> >> > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM  >
> >> > wrote:
> >> >
> >> >> i want calculate the secondary structure of protein in gromacs.but
> >> >> when i am using this command
> >> >>
> >> >> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
> >> >>
> >> >> getting this error
> >> >> Program do_dssp, VERSION 4.5.5
> >> >> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c,
> >> line:
> >> >> 572
> >> >>
> >> >> Fatal error:
> >> >> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7
> >
> >> >> /dev/null 2> /dev/null
> >> >> For more information and tips for troubleshooting, please check the
> >> >> GROMACS
> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >>   how i will solve this problem.please help me
> >> >> --
> >> >> Gromacs Users mailing list
> >> >>
> >> >> * Please search the archive at http://www.gromacs.org/
> >> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >> >>
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> >> >>
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> >> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >> >> send a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] secondary structure analysis

2018-05-16 Thread SHAHEE ISLAM

when i am using command
dssp -h
below are shown on the terminal screen
DSSP 2.0.4 options:
  -h [ --help ] Display help message
  -i [ --input ] argInput file
  -o [ --output ] arg   Output file, use 'stdout' to output to screen
  -v [ --verbose ]  Verbose output
  --version Print version
  -d [ --debug ] argDebug level (for even more verbose output)


Examples:

To calculate the secondary structure for the file 1crn.pdb and
write the result to a file called 1crn.dssp, you type:

  dssp.exe -i 1crn.pdb -o 1crn.dssp

but when i am trying
dssp.exe -i 5B1F2.PDB -o 1crn.dssp
error is
dssp.exe: command not found
thanking you

On 5/16/18, Joe Jordan  wrote:
> Have you tried running the dssp command on a pdb file to ensure that it is
> working as intended? FYI 4.5.5 is no longer supported so you may want to
> consider upgrading to (the much faster) gromacs 2018.
>
> On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM 
> wrote:
>
>> i have installed dssp2.04 in usr/local/bin.
>>
>> On 5/16/18, Joe Jordan  wrote:
>> > You have to point to where you have dssp installed. This may require
>> > you
>> to
>> > install dssp.
>> >
>> > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM 
>> > wrote:
>> >
>> >> i want calculate the secondary structure of protein in gromacs.but
>> >> when i am using this command
>> >>
>> >> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
>> >>
>> >> getting this error
>> >> Program do_dssp, VERSION 4.5.5
>> >> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c,
>> line:
>> >> 572
>> >>
>> >> Fatal error:
>> >> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
>> >> /dev/null 2> /dev/null
>> >> For more information and tips for troubleshooting, please check the
>> >> GROMACS
>> >> website at http://www.gromacs.org/Documentation/Errors
>> >>   how i will solve this problem.please help me
>> >> --
>> >> Gromacs Users mailing list
>> >>
>> >> * Please search the archive at http://www.gromacs.org/
>> >> Support/Mailing_Lists/GMX-Users_List before posting!
>> >>
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
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>> >> send a mail to gmx-users-requ...@gromacs.org.
>> >>
>> >
>> >
>> >
>> > --
>> > Joe Jordan
>> > --
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>>
>
>
>
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Re: [gmx-users] Regarding MD simulations involving metal ion (Mn)

2018-05-16 Thread Paul bauer


Hello,

for metal ions (and especially transition metals) you should first 
consider what kind of metal model you want to employ, as the different 
models (bonded, soft sphere or dummy model) have have different properties.
There are numerous papers outlining the parametrization of those 
different models, so you can search them once you have decided on how 
you want to model the ion :)


If you are in need of modelling things such as unpaired electrons, spin 
effects or anything else quantum mechanical, you should consider if MD 
is the correct approach to simulate a structure like this or if a pure 
QM description is more appropriate.


If you have a reference for a similar system you should follow the 
approach outlined there as much as possible.


Also one note of caution, you should only use one force field to 
simulate your system, and never mix and match force fields.


Cheers

Paul

On 16/05/18 11:57, dhaval patel wrote:

Dear All,

I need to simulation of protein-ligand with coordinated metal ion bound to
ligand. The metal ion is Mn+2, Advise me whether its correct to use
CHARMM36 and OPLSS force field for parameterization? What things should
taken care while simulating such cases where we have metals with unpaired
electrons?   Any help is  highly appreciated.



Sincerely yours,
Dhaval



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Re: [gmx-users] secondary structure analysis

2018-05-16 Thread Joe Jordan

Have you tried running the dssp command on a pdb file to ensure that it is
working as intended? FYI 4.5.5 is no longer supported so you may want to
consider upgrading to (the much faster) gromacs 2018.

On Wed, May 16, 2018 at 11:45 AM, SHAHEE ISLAM 
wrote:

> i have installed dssp2.04 in usr/local/bin.
>
> On 5/16/18, Joe Jordan  wrote:
> > You have to point to where you have dssp installed. This may require you
> to
> > install dssp.
> >
> > On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM 
> > wrote:
> >
> >> i want calculate the secondary structure of protein in gromacs.but
> >> when i am using this command
> >>
> >> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
> >>
> >> getting this error
> >> Program do_dssp, VERSION 4.5.5
> >> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c,
> line:
> >> 572
> >>
> >> Fatal error:
> >> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
> >> /dev/null 2> /dev/null
> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> website at http://www.gromacs.org/Documentation/Errors
> >>   how i will solve this problem.please help me
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
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> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-requ...@gromacs.org.
> >>
> >
> >
> >
> > --
> > Joe Jordan
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[gmx-users] Regarding MD simulations involving metal ion (Mn)

2018-05-16 Thread dhaval patel

Dear All,

I need to simulation of protein-ligand with coordinated metal ion bound to
ligand. The metal ion is Mn+2, Advise me whether its correct to use
CHARMM36 and OPLSS force field for parameterization? What things should
taken care while simulating such cases where we have metals with unpaired
electrons?   Any help is  highly appreciated.



Sincerely yours,
Dhaval
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Re: [gmx-users] secondary structure analysis

2018-05-16 Thread SHAHEE ISLAM

i have installed dssp2.04 in usr/local/bin.

On 5/16/18, Joe Jordan  wrote:
> You have to point to where you have dssp installed. This may require you to
> install dssp.
>
> On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM 
> wrote:
>
>> i want calculate the secondary structure of protein in gromacs.but
>> when i am using this command
>>
>> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
>>
>> getting this error
>> Program do_dssp, VERSION 4.5.5
>> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line:
>> 572
>>
>> Fatal error:
>> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
>> /dev/null 2> /dev/null
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>   how i will solve this problem.please help me
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
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>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-requ...@gromacs.org.
>>
>
>
>
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Re: [gmx-users] secondary structure analysis

2018-05-16 Thread Joe Jordan

You have to point to where you have dssp installed. This may require you to
install dssp.

On Wed, May 16, 2018 at 11:41 AM, SHAHEE ISLAM 
wrote:

> i want calculate the secondary structure of protein in gromacs.but
> when i am using this command
>
> do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10
>
> getting this error
> Program do_dssp, VERSION 4.5.5
> Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line:
> 572
>
> Fatal error:
> Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
> /dev/null 2> /dev/null
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>   how i will solve this problem.please help me
> --
> Gromacs Users mailing list
>
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> Support/Mailing_Lists/GMX-Users_List before posting!
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[gmx-users] secondary structure analysis

2018-05-16 Thread SHAHEE ISLAM

i want calculate the secondary structure of protein in gromacs.but
when i am using this command

do_dssp -f dynamic.xtc -s dynamic.tpr -sc scount.xvg -o ss.xpm -dt 10

getting this error
Program do_dssp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572

Fatal error:
Failed to execute command: /usr/local/bin/dssp -na ddsbJ3bY ddT7Ubn7 >
/dev/null 2> /dev/null
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
  how i will solve this problem.please help me
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[gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Naba

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y
pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.

waiting for your great help..
Nabajyoti Goswami
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
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Re: [gmx-users] Pulling two groups in opposite direction

[gmx-users] Protein protein complex simulation to be done with respect to observe changes in temperature

[gmx-users] partial exclusion of interactions within 1-4

Re: [gmx-users] Pulling two groups in opposite direction

Re: [gmx-users] C6-C12 table potential

Re: [gmx-users] C6-C12 table potential

[gmx-users] C6-C12 table potential

[gmx-users] Topology file

Re: [gmx-users] secondary structure analysis

Re: [gmx-users] secondary structure analysis

Re: [gmx-users] Regarding MD simulations involving metal ion (Mn)

Re: [gmx-users] secondary structure analysis

[gmx-users] Regarding MD simulations involving metal ion (Mn)

Re: [gmx-users] secondary structure analysis

Re: [gmx-users] secondary structure analysis

[gmx-users] secondary structure analysis

[gmx-users] Pulling two groups in opposite direction

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