AMBER Archive (2006)

Subject: AMBER: Problems amber mask in distance?

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Nov 08 2006 - 10:39:18 CST

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

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