AMBER Archive (2006)

Subject: Re: AMBER: Problem with mask when using distance in ptraj

From: Christopher Gaughan (clgaughan68_at_gmail.com)
Date: Sun Nov 26 2006 - 08:28:29 CST

Thanks for the advice.

I have indeed tried all of the combinations you suggest- none have worked so
far. However, when I use printAtoms command in rdparm I get the following:

RDPARM MENU: printAtoms
Mask [] represents 10 atoms
Perturbation is ON Perturbed atom
information
Number: Atom Charge Mass ( Residue ) Type Tree Atom Charge (
Residue ) Type
     1: 7 0.93956 6.6 ( 1: 40) 10 73
     2: .381 0.43030 27.3 ( 1: 40) .932 .839
     3: 27 1.50925 19.6 ( 1: 40) 10 3
     4: .740 1.02841 5.7 ( 1: 40) .757 .571
     5: 16 0.47239 27.6 ( 1: 40) 73 21
     6: .591 1.47830 19.0 ( 1: 40) .928 .242
     7: 6 1.05755 6.5 ( 1: 40) 9 74
     8: .879 0.44868 26.2 ( 1: 40) .542 .256
     9: 26 1.56616 19.7 ( 1: 40) 11 4
    10: .181 1.02654 6.7 ( 14:.109) .201 .28

It would seem as though I had only 10 atoms in the file. However, it should
have enough atoms for two 28 amino acid alpha helices- 56 residues. Maybe
this is why I cant specify a mask?

Thanks again
Chris

On 11/22/06, Thomas Cheatham <tec3_at_utah.edu> wrote:
>
>
> > > Mask [@CA:244] represents 0 atoms !!!NO ATOMS DETECTED!!!
> >
> > You can use the ambmask command to play around with various masks to get
> > what you want. Have you tried ':544_at_CA'? All the examples in the
> Users'
> > Manual have the residue specification to the left of the atom
> specification,
> > and maybe that is required(?).
>
> Yes, residue specification must be first. Also, there is a "checkmask"
> command in the "rdparm" version of ptraj.
>
> rdparm prmtop
> checkmask :244_at_CA
> quit
>
>
>
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