Sergey,
try to use the 'old mask' syntax, such that you specify two atoms as in:
distance num73 .540,1038 :73.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.O out ASP34_ASN66/ASP34_73.out
> distance num74 '.540 | .1038' :74.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.O out ASP34_ASN66/ASP34_73.out
> Mask [.540 | .1038] represents 2 atoms
> Mask [:73.O] represents 1 atoms
>
> PTRAJ: distance num74 '.540 | .1038' :74.O out ASP34_ASN66/ASP34_74.out
> Mask [.540 | .1038�] represents 1 atoms
> Mask [:74.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.CG,:66.ND2
> Atom selection 2 is :73.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.CG
> Atom selection 2 is :74.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.CG | :66.ND2' :73.O out ASP34_ASN66/ASP34_73.out
> distance num74 ':34.CG | :66.ND2' :74.O out ASP34_ASN66/ASP34_74.out
>
> I get something similar wrong:
>
> PTRAJ: distance num73 ':34.CG | :66.ND2' :73.O out
> ASP34_ASN66/ASP34_73.out
> Mask [:34.CG | :66.ND2] represents 2 atoms
> Mask [:73.O] represents 1 atoms
>
> PTRAJ: distance num74 ':34.CG | :66.ND2' :74.O out
> ASP34_ASN66/ASP34_74.out
> Mask [:34.CG | :66.ND2 ] represents 26 atoms
> Mask [:74.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.CG,:66.ND2
> Atom selection 2 is :73.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.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
>
>
>
>
>
>
>
>
>
>
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--
===================================================================
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.sunysb.edu
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Received on Sun Nov 12 2006 - 06:07:10 PST
