Re: ABF with the RMSD colvar

From: George Patargias (gpat_at_bioacademy.gr)
Date: Wed Apr 16 2014 - 05:14:05 CDT

Hi Giacomo,

Sorry for the hassle; just one more question on this particular ABF
calculation.

If I want to study the conformational transition A --> B and use
the structure of B as a reference for the RMSD colvar, is the ABF bias
going to "drive" the RMSD of A with respect to B from the upperboundary
value (that I will calculate by superimposing A and B) to the
lowerboundary
value (a small one, like 0.1)?

George

> Yes, avoid using wrapAll in this case. Non covalently linked protein
fragments would be wrapped individually, and mess up the calculation of
the
> RMSD.
> Giacomo
> On Tue, Apr 15, 2014 at 6:22 AM, George Patargias
> <gpat_at_bioacademy.gr>wrote:
>> Hello,
>> I am trying to set up an ABF calculation using the RMSD colvar. The
atom
>> block of the colvar configuration file contains all the C-alpha atoms
of
>> a
>> protein complex that consists of 7 (non covalently linked) subunits. I
am trying to decide whether I need to exclude the wrapAll option (and
use only wrapWater) on the basis of the recommendations found here
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html#SECTION000132410000000000000
I would really appreciate any tips on this
>> Thanks!
>> Dr. George Patargias
>> Postdoctoral Research Fellow
>> Biomedical Research Foundation
>> Academy of Athens
>> 4, Soranou Ephessiou
>> 115 27
>> Athens
>> Greece
>> Office: +302106597568

Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568

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