VMD-L Mailing List

From: caldwell_at_heimdal.compchem.ucsf.edu
Date: Thu Jul 31 2003 - 14:22:12 CDT

Please be aware that Amber has two coordinate file formats:

inpcrd/restrt is the single structure file that contains the
high resolution coordinates. It is used to start/restart
minimization/dynamics runs in conjuction with prmtop.

mdcrd is the multiple structure (lower resolution) trajectory file.

They are NOT interchangeable.

VMD reads only mdcrd files. If you want to look at a single
structure from your inpcrd/restrt file then convert it to
a pdb file with one of the utilities included in Amber.

jim

On 31 Jul 2003, Teletchéa Stéphane wrote:

> Le lun 28/07/2003 à 22:45, Anshul Shah a écrit :
> > Hi all,
> >
> > I am a new user of VMD and Amber. I am having a problem that sounds
> > similar to something I read in the list archives. When I try to open
> > Amber 7.0 format .prmtop and .inpcrd files in VMD 1.8.1, the molecule I
> > get is very much distorted; that is, the bonds are very obviously not in
> > their proper configuration. The original .pdb file looks fine in VMD,
> > but I get this problem after using Amber Leap to generate the .prmtop
> > and .inpcrd files. It seems that either Leap went wrong, or VMD is not
> > using the two files correctly. Does anyone what this problem might be,
> > or how I can fix it?
> >
> > Thanks,
> > Anshul
>
> This is a bug of vmd reader, it has a problem for reading single crd
> files.
> The problems comes from amber's denomination which is quite untrivial.
>
> When you build a structure, you get a inpcrd file :
> ---------------------------------------------------------------------
> Format description :
> FORMAT(20A4) ITITL
> ITITL : the title of the current run, from the AMBER
> parameter/topology file
>
> FORMAT(I5,5E15.7) NATOM,TIME
> NATOM : total number of atoms in coordinate file
> TIME : option, current time in the simulation (picoseconds)
>
> FORMAT(6F12.7) (X(i), Y(i), Z(i), i = 1,NATOM)
> X,Y,Z : coordinates
> IF dynamics
> FORMAT(6F12.7) (VX(i), VY(i), VZ(i), i = 1,NATOM)
> VX,VY,VZ : velocities (units: Angstroms per 1/20.455 ps)
> IF constant pressure (in 4.1, also constant volume)
> FORMAT(6F12.7) BOX(1), BOX(2), BOX(3)
> BOX : size of the periodic box
>
>
> example :
> [stephane_at_pc-54-149 crd]$ head file.crd
> Titre du fichier base.linkin
> 629
> -0.8080000 -8.8730001 -2.0799999 0.2700000 -7.7249999 -1.8300000
> ...
>
> ---------------------------------------------------------------------
>
> When you run a dynamics you get a mdcrd file.
> Format description :
> FORMAT(20A4) ITITL
> ITITL : the title of the current run, from the AMBER
> parameter/topology file
> The following snapshot is written every NTWX steps in the trajectory
> (specified in the control input file):
> FORMAT(10F8.3) (X(i), Y(i), Z(i), i=1,NATOM)
> X,Y,Z : coordinates or velocities (velocity units: Angstroms per 1/20.455 ps)
>
> example :
> [stephane_at_pc-54-149 crd]$ head file.rst
> Titre du fichier base.linkin
> 0.323 -9.832 -4.264 0.818 -9.366 -3.245 2.027 -8.556
> -3.295 2.020
>
> ---------------------------------------------------------------------
>
> To complicate it, can have box info size, so you get 4 possibilities.
>
> VMD reads the second but not the first correctly (it names it crd, but
> in reality it is rather a mdcrd/rst file).
>
> 'Removing the first line of the inpcrd trick' works only because the
> difference between inpcrd and mdcrd/rst is essentially the
> FORMAT(I5,5E15.7) NATOM,TIME which is different.
> Nevertheless, file formats are quite different : 6 columns for inpcrd
> with 7 decimals precision and 10 columns for mdcrd/rst with 3 decimals
> precision.
>
> So the vmd reader has never completely read the inpcrd correctly but
> removing the first line helps this, even if in that cas i'm not sure of
> the internal precision it uses -certainly not essential for
> visualisation-.
>
> Finally, amber 7 has switched to another parameter file, so you now hqve
> another degree of complexity ...
>
> I'm ready to provide other examples as required to fix this annoying
> bug.
>
> For VMD developpers, there is a description of amber formats in
> http://amber.scripps.edu/formats.html
>
> Stef
>
> 

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