AMBER Archive (2008)

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

From: Marta Rossini (marta.rossini_at_live.com)
Date: Mon Mar 31 2008 - 07:57:04 CDT

Ok, sorry for the very basic questions (I'm a beginner),
this is what I meant, but now I obtain an "ERROR: syntax error" when I type the command relax also if I try to reproduce your example! I loaded leaprc.ff99 at the startup, and I don't understand what is wrong...

----------------------------------------
> Date: Mon, 31 Mar 2008 13:19:49 +0200
> From: fyd_at_q4md-forcefieldtools.org
> To: amber_at_scripps.edu
> Subject: RE: AMBER: Select specific residues (leap)
>
> Quoting Marta Rossini :
>
>> 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 :
>>>
>>>> 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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