Re: preparation of amber topology file in carma

[Nicholas M. Glykos]

> I am Aashish Bhatt form INST-Mohali(India). Sir in my system we used amber
> topology file instead of namd PSF file but we run the simulation in namd
> (dcd file). Can we use the amber topology file in carma for cross-correlation?
>
> the error we got
> *Unidentified keyword or argument: topo.prmtop. Abort.*

Use VMD (from a unix shell) to prepare a PSF file as follows :



vmd -dispdev text test.prmtop test.crd

set solvent [atomselect top solvent]
$solvent set segname W
set protein [atomselect top protein]
$protein set segname A
set ions [atomselect top ions]
$ions set segname I
set all [atomselect top all]
$all writepsf test.psf
quit



Then edit the resulting PSF file with an editor and confirm that VMD
correctly assigned chain identifiers (SEGIDs) to protein/ions/water/...

If there are problems with the SEGID assignments, you'll have to manually
correct them.




ps. Please use the carma mailing list for correspondence related to
carma/grcarma.


--


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/