[gmx-users] Water-Mediated Hydrogen Bonds

[Raja Pandian]

Dear All,



I’m doing research in the field of Protein-DNA interaction. I have gone
through these papers,

*A “Solvated Rotamer” Approach to Modeling Water-Mediated Hydrogen Bonds at
Protein–Protein Interfaces*

*“Effect on DNA relaxation of the single Thr718Ala mutation in human
topoisomerase I: a functional and molecular dynamics study”*

*“Molecular Dynamics Simulation Study of Interaction between Model Rough
Hydrophobic Surfaces.”*

*“Prediction of Protein Binding to DNA in the Presence of Water-Mediated
Hydrogen Bonds”*



I have found lot of interesting things on these papers that will be useful
for the progress of my research carrier.

I have been looking for water mediated hydrogen bond in my simulation when i
use g_hbond the -ins option it dose not showing the water mediated hydrogen
bond could you please tell me how to get the hydrogen mediated hydrogen bond
and water mediated free energy in Gromacs ?

Is there any way to calculate water mediated hydrogen bond between
Protein-DNA using Gromacs tools?

If it is possible, please send your program (water mediated hydrogen bond
derivation program) to me and also the program operating procedure.



Eagerly waiting for your reply.

Thanking You



Faithfully

Raja
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Re: [gmx-users] Gromacs to Amber trajectory

[Raja Pandian]

Dear All,

I have created Amber input file (.prmtop and .rst7) using Xleap. And then I
have converted this input file into Gromacs input file format (*.gro and
*.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber
Force Field). Now I would like to convert Gromacs trajectory file to Amber
trajectory file format. So that I can easily analyses this trajectory. I
tried to convert Gromacs (.xtc) trajectory file to Amber (.mdcrd) trajectory
file using VMD. This VMD converted trajectory is not working fine for DCCM
(Dynamic cross correlation Matrix) analysis.

Now i'm trying to convert Gromacs trajectory into dcd format, and then use
ptraj to read the dcd file and write the mdcrd  (or AMBER netcdf)
trajectory.



Example:

---

 [1] Gromacs20ns.xtc à nojump.xtc (using trjcat/trjconv)

[2] nojump.xtc à amber20ns.dcd (using VMD)

[3] Ptraj file conversion

trajin amber20ns.dcd

trajout amber20ns.nc netcdf

(or)

Is it necessary to do image for this file.



trajin test.dcd

center origin

image origin center

trajout amber20ns.nc netcdf



Is this correct procedure?



I want to do DCCM (Dynamic cross correlation analysis).

DCCM Ptraj file



trajin test.rst7

trajin amber20ns.nc

strip :WAT

strip :Cl-

center :1-85 origin

image origin center

matrix correl name corr @CA out amber20ns.dccm byres



If you have any ptraj file format for this.

 Actually i did simulation based on NPT ensemble. Is it necessary to mention
the BOX dimensions in any were in the dcd file creation?

Already i tried to convert Gromacs trajectory into PDB (total trajectory)
but it is not working well for the analysis purpose of AMBER.


Eagerly waiting for your suggestion

Regards
Raja



On Fri, Jun 17, 2011 at 6:46 AM, Mark Abraham wrote:

> **
> On 17/06/2011 2:57 AM, Raja Pandian wrote:
>
>
>
> Dear All,
>
> I have created Amber input file (.prmtop and .rst7) using Xleap. And then I
> have converted this input file into Gromacs input file format (*.gro and
> *.top) with amb2gmx.pl script. I did simulation using Gromacs Package
> (Amber Force Field). Now I would like to convert Gromacs trajectory file to
> Amber trajectory file format. So that I can easily analyses this trajectory.
> I tried to convert Gromacs trajectory file to Amber trajectory file using
> VMD. This VMD converted trajectory is not working fine. Pls help me in this
> regards
>
>
> You really haven't said what you've done at the critical point, nor why you
> think it is not working. So we are unable to help at this time.
>
> Maek
>
> --
> gmx-users mailing listgmx-users@gromacs.org
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> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>
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[gmx-users] Gromacs to Amber trajectory

[Raja Pandian]

Dear All,

I have created Amber input file (.prmtop and .rst7) using Xleap. And then I
have converted this input file into Gromacs input file format (*.gro and
*.top) with amb2gmx.pl script. I did simulation using Gromacs Package (Amber
Force Field). Now I would like to convert Gromacs trajectory file to Amber
trajectory file format. So that I can easily analyses this trajectory. I
tried to convert Gromacs trajectory file to Amber trajectory file using VMD.
This VMD converted trajectory is not working fine. Pls help me in this
regards

Eagerly waiting for your suggestion.



Regards

Raja
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