Convert Amber.prmtop to .psf for Carma input

[Fulbabu]

Dear All,

I have Amber MDEngine topology (prmtop) and coordinate (inpcrd) file and all the simulation trajectory (mdcrd) file.

From these files how can I get Carma input file like (psf and dcd)?

Please somebody give me some idea or script from that I get those file easily.

Thank in Advance

Fulbabu  

[Nicholas M. Glykos]

> I have Amber MDEngine topology (prmtop) and coordinate (inpcrd) file and
> all the simulation trajectory (mdcrd) file.
> From these files how can I get Carma input file like (psf and dcd)?
> Please somebody give me some idea or script from that I get those file
> easily.

Getting the .psf is easy but requires some editing. Using VMD it would go
like this :

vmd -dispdev text test.prmtop test.crd
set all [atomselect top all]
$all writepsf ionized.psf
quit

Then, edit the PSF with your favorite editor to add meaningful SEGIDs.



For converting the trajectory file, cpptraj appears to be able to do the
trick (haven't tested it myself).




--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, https://utopia.duth.gr/glykos/

[Fulbabu]

Is there any other way to use Carma directly from AMBER file (prmtop and mdcrd) ?

[Nicholas M. Glykos]

> Is there any other way to use Carma directly from AMBER file (prmtop and
> mdcrd) ?

No. Carma can only read PSF/DCD files.

[Fulbabu Sk]

Got it.

***************
Kind regards

Md Fulbabu Sk

Ph.D. Research Scholar
Discipline of BioSciences and Biomedical Engineering (BSBE)
Indian Institute of Technology Indore (IITI), India

Computational BioPhysics Group IITI (Kar's Lab)