AMBER Archive (2006)

Subject: Re: AMBER: Problems amber mask in distance?

From: Viktor Hornak (hornak_at_csb.sunysb.edu)
Date: Wed Nov 08 2006 - 10:50:59 CST

Sergey,

try to use the 'old mask' syntax, such that you specify two atoms as in:

distance num73 @540,1038 :73_at_O out ASP34_ASN66/ASP34_73.out

First, logical operators (e.g. |) were not implemented in amber8.
Second, the 'new mask' syntax implemented in amber9 would allow brackets
and logical operators but is very likely broken and needs to be fixed
(which I should do :-()...

Cheers,
-Viktor

Sergey Samsonov wrote:
> Dear AMBERs,
>
> I was using distance command to calculate the distance between center
> of mass of two atoms and the third atom.
>
> distance num73 '@540 | @1038' :73_at_O out ASP34_ASN66/ASP34_73.out
> distance num74 '@540 | @1038' :74_at_O out ASP34_ASN66/ASP34_74.out
>
> The output is really weird since it's correctly calculating the
> distance in the first case and uses just first atom in the mask
> (though the lines are completely identical) for the second line and
> the following lines of this kind.
>
>
> PTRAJ: distance num73 '@540 | @1038' :73_at_O out ASP34_ASN66/ASP34_73.out
> Mask [@540 | @1038] represents 2 atoms
> Mask [:73_at_O] represents 1 atoms
>
> PTRAJ: distance num74 '@540 | @1038' :74_at_O out ASP34_ASN66/ASP34_74.out
> Mask [@540 | @1038�] represents 1 atoms
> Mask [:74_at_O] represents 1 atoms
>
> ...
>
> ACTIONS
> 1> DISTANCE: between the atoms selections center of mass will be
> saved to array named num73
> Atom selection 1 is :34_at_CG,:66_at_ND2
> Atom selection 2 is :73_at_O
> Data will be dumped to a file named ASP34_ASN66/ASP34_73.out
> 7> DISTANCE: between the atoms selections center of mass will be
> saved to array named num74
> Atom selection 1 is :34_at_CG
> Atom selection 2 is :74_at_O
> Data will be dumped to a file named ASP34_ASN66/ASP34_74.out
>
> One can notice the point after @1038 in the second case though there
> is no point in input,
> I had reqritten that several times.
>
> If I use another mask for the same sake:
>
> distance num73 ':34_at_CG | :66_at_ND2' :73_at_O out ASP34_ASN66/ASP34_73.out
> distance num74 ':34_at_CG | :66_at_ND2' :74_at_O out ASP34_ASN66/ASP34_74.out
>
> I get something similar wrong:
>
> PTRAJ: distance num73 ':34_at_CG | :66_at_ND2' :73_at_O out
> ASP34_ASN66/ASP34_73.out
> Mask [:34_at_CG | :66_at_ND2] represents 2 atoms
> Mask [:73_at_O] represents 1 atoms
>
> PTRAJ: distance num74 ':34_at_CG | :66_at_ND2' :74_at_O out
> ASP34_ASN66/ASP34_74.out
> Mask [:34_at_CG | :66_at_ND2 ] represents 26 atoms
> Mask [:74_at_O] represents 1 atoms
>
> ACTIONS
> 1> DISTANCE: between the atoms selections center of mass will be
> saved to array named num73
> Atom selection 1 is :34_at_CG,:66_at_ND2
> Atom selection 2 is :73_at_O
> Data will be dumped to a file named ASP34_ASN66/ASP34_73.out
> 7> DISTANCE: between the atoms selections center of mass will be
> saved to array named num74
> Atom selection 1 is :34,:66
> Atom selection 2 is :74_at_O
> Data will be dumped to a file named ASP34_ASN66/ASP34_74.out
>
> Somehow the space after @NH2 is appearing in the second case, but
> again, there is no space in the input.
>
> I have rewritten the lines for several times and they are really
> identical so I cannot understand what could be wrong.
> I also installed the patch bugfix.all for AMBER 8, but nothing
> changed. Of course, I can calculate the distance several times
> with several inputs but I'd like to calculate rmany distances
> simultaneously.
>
> I'll appreciate any help very much.
>
> Thank you in advance!
>
> Sergey
>
>
>
>
>
>
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
===================================================================
Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail: viktor.hornak_at_sunysb.edu
=================================================================== 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu