AMBER Archive (2006)

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

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Wed Nov 08 2006 - 10:57:20 CST

Thank you very much, Viktor!

It seems it does work now. Also I tried '||' instead of '|' and it did
the same as just in case of comma between atomic numbers.

Sergey

Viktor Hornak wrote:
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
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>

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