From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Fri Sep 24 2010 - 04:59:59 CDT
Hi Marc,
You can obtain this result with the following syntax:
psfSegID PEPA PEPB
atomNameResidueRange CA 5-315
atomNameResidueRange CA 5-315
Each instance of atomNameResidueRange applies to one segment identifier in
the list.
Cheers,
Jerome
On 24 September 2010 10:44, Marc Baaden <baaden_at_smplinux.de> wrote:
>
> Hi Jerome,
>
> Thank you for these explanations.
>
> The behavior concerning psfSegID is indeed corrected in 2.7b4, meaning
> that if I specify atomNumbers, I am no longer required to also specify
> psfSegID.
>
> While we are at it, a couple of feature requests, if you were to revise
> this behavior at some point:
>
> - one could make the psfSegID related to the previous
> atomNameResidueRange command, in order to allow one to use several of
> these statements in an atom group definition, as in
>
> atomNameResidueRange CA 5-315
> psfSegID PEPA
> atomNameResidueRange CA 5-315
> psfSegID PEPB
> [..]
>
> - even easier would be wildcarding, such as in
>
> atomNameResidueRange CA 5-315
> psfSegID PEP*
>
> or
>
> atomNameResidueRange CA 5-315
> psfSegID PEP?
>
> Thanks,
> Marc
>
>
> jhenin_at_ifr88.cnrs-mrs.fr said:
> >> I also noticed a bug in the definition of the atom groups. I have a >
> >> multimeric protein, with each chain called "PEPA", "PEPB",.. ; I want
> >> > all Calpha atoms of all chains, and don't want to use the
> >> "psfSegID" > specification. But if I don't include it, NAMD complains
> >> and doesn't > start. On the other hand, the atom numbers seem to be
> >> properly taken > into account (eg also those not in segID PEPA are
> >> counted). THis seems > to be a but to me. > > It's also a bit
> >> unfortunate that one cannot use several segment > identifiers as in
> >> all Calphas of PEPA, PEPB, etc. >
>
> >> Does that still happen using the newly released 2.7b4? I fixed some
> >> problems there, but if I have created new ones, I should fix them
> >> asap.
>
>
> --
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden_at_smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>
>
>
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