AMBER Archive (2007)

Subject: Re: AMBER: restraints to individual atoms

From: Eddie Men (pckboy_at_gmail.com)
Date: Tue Nov 27 2007 - 21:54:30 CST

Thanks Ross!

This works like a charm...sometimes it is hard for me to find the
right info in the manual :(

It works all tight now :)

Eddie

Ross Walker wrote:
> Hi Eddie,
>
>
>> restraintmask=':541,542,543'
>>
>> I would like however, to make a restrain on atoms within the
>> specified
>> restraintmask residues,
>> I know that for the qm/mm region it is possible to pick
>> atoms instead of
>> residues, but what
>> about the restraintmask section?.
>>
>
> You can pick individual atoms in the mask using the @symbol. So for example:
>
> restraintmask=':5-7 | @121-124,155,157',
>
> Would select atoms that were either part of residues 5,6,7 OR were atom
> numbers 121,122,123,124,155,157.
>
> I believe that this is not an exclusive or and so you can have atom numbers
> that overlap with the residue selections. Although I haven't tested this.
> For a full description of the ambmask language see page 287-288 of the Amber
> 9 manual.
>
> Good luck,
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
> be read every day, and should not be used for urgent or sensitive issues.
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu