AMBER Archive (2008)

Subject: RE: AMBER: Select specific residues (leap)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Mar 31 2008 - 06:19:49 CDT

Quoting Marta Rossini <marta.rossini_at_live.com>:

> I'm sorry, but I already read these tutorials and I didn't find any
> example about the correct syntax to use in order to select entire
> residues (and not single atoms) on the basis of their residue
> numbers (and not names, that is, not "all" alanines and so on...)

I think you need to read the introduction of LEaP in the AMBER manual,
and do the connection between what is written in this manual and the
q4md-forcefieldtools.org tutorial. I just did:

TEST = sequence { ACE ALA ALA NME }
# select the residue number 2
select TEST.2
relax TEST
deselect TEST

For "select", you can use:
select molecule
          or
select molecule.residue
          or
select molecule.residue.atom

regards, Francois

>> Quoting Marta Rossini <marta.rossini_at_live.com>:
>>
>> > I want to relax specific residues in a protein, but it's very
>> > complicate to select them manually using xleap interface. Is there a
>> > command to select specific residues (es: ALA32) in xleap or in
>> > tleap too (since the function "relax" has been included in tleap)
>> > and include them into a unit?
>>
>> Please see:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
>> &
>> http://q4md-forcefieldtools.org/Tutorial/leap.php
>>
>> regards, Francois

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