Re: Colvars and COM restraints for protein+membrane; plus a minor bug

From: Marc Baaden (
Date: Fri Sep 24 2010 - 03:44:41 CDT

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

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*


  atomNameResidueRange CA 5-315
  psfSegID PEP?

  Marc 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      -
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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