AMBER Archive (2008)

Subject: Re: AMBER: ptraj selection

From: David Watson (dewatson_at_olemiss.edu)
Date: Thu Jul 10 2008 - 01:01:01 CDT

On Jul 9, 2008, at 11:27 PM, Ilyas Yildirim wrote:

> On Wed, 9 Jul 2008, David Watson wrote:
>
>> On Jul 9, 2008, at 10:13 PM, Ilyas Yildirim wrote:
>>
>>> On Wed, 9 Jul 2008, David Watson wrote:
>>>
>>>> On Jul 9, 2008, at 8:07 PM, Ilyas Yildirim wrote:
>>>>> Can someone tell me what the mistake in the ptraj script is?
>>>>> Thanks
>>>>> a lot.
>>>>>
>>>>
>>>> I think the problem lies with the use of quotes and parentheses.
>>>
>>> Can you explain a little bit more? If I do not use the quotes and
>>> paranthesis, ptraj won't read the part after the first '|'. Thanks.
>>>
>>
>> I can only refer you to the 'ambmask' section of the Amber Users'
>> Manual, as that is all that I can find on the matter.
>> Braces are definitely verboten, whereas parentheses are permitted,
>> but
>> I don't see where quotes are permitted.
>>
>> Perhaps use the parentheses without quotes?
>>
>
> The quotes does not look like to create the problem. According to the
> manual, the mask should be enclosed in double quotes if the new
> parser is
> used (pp 245, Section 10.1).
>

As far as the manual is concerned, I see no mention of the 'atommask'
section anywhere in the AMBER 9 documentation except for on that very
same page, with respect to the usage of the new parser.
If there is something that you need to do that is not covered by the
'old parser', maybe you could explain it to Ross and David and maybe
they could tell you why 'atommask' is not documented (other than not
having volunteers to write such documentation).

As far as using atom types with single quotes, perhaps you should try
removing those, too.

> I am trying to follow the information given in $AMBERHOME/src/ptraj/
> mask.c
> because the mask part of ptraj in the manual is not clear.
>
>
> ------------ $AMBERHOME/src/ptraj/mask.c ----------------------
> .
> .
> .
> * The syntax for elementary selections is the following
> * :{residue numlist} e.g. [:1-10] [:1,3,5] [:1-3,5,7-9]
> * :{residue namelist} e.g. [:LYS] [:ARG,ALA,GLY]
> * @{atom numlist} e.g. [@12,17] [@54-85] [@12,54-85,90]
> * @{atom namelist} e.g. [@CA] [@CA,C,O,N,H]
> * @/{element namelist} e.g. [@/H] [@/C,H]
> * :* means all residues and @* means all atoms
> *
> * The matching is case sensitive.
> *
> * compound expressions of the following type are allowed:
> * :{residue numlist | namelist}@{atom namelist | numlist | typelist}
> * and are processed as (i.e. replaced by two AND'ed expressions):
> * :{residue numlist | namelist} & @{atom namelist | numlist |
> typelist}
> * e.g. :1-10_at_CA is equivalent to :1-10 & @CA
> * :LYS@/H is equivalent to :LYS & @/H
> *
> * more examples:
> * :ALA,TRP ... all alanine and tryptophane residues
> * :5,10_at_CA ... CA carbon in residues 5 and 10
> * :* & !@/H ... all non-hydrogen atoms (equivalent to "!@/H")
> * @CA,C,O,N,H ... all backbone atoms
> * !@CA,C,O,N,H ... all non-backbone atoms (=sidechains for proteins
> only)
> * :1-500_at_O & !(:WAT | :LYS,ARG)
> * ... all backbone oxygens in residues 1-500 but not in
> * water, lysine or arginine residues
> .
> .
> .
> -------------------------------------------------------
>
> According to these examples, I do not see any mistake with the mask
> "(:1-4_at_C1',C2',C3',C4',C5',O4',O5',O3',P) | (:1,2_at_N9,C8,C4) |
> (:3,4_at_N1,C2,C6)". Thanks again.
>
> --
> Ilyas Yildirim
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