From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Feb 22 2017 - 11:57:14 CST
Yup, its zero based. This corresponds to taking the "index" from VMD, rather than the serial, or equivalently one less than the index in the pdb.
On 02/21/2017 04:48 PM, Lara rajam wrote:
I would like to use the torsional restraints in the simulation.
I would like to know how the atom numbers should be given in order.
For eg., when we write a solvated and counterion added pdb, do we need to take the respective atom number by looking in to it. But, when I read the constraints and Restraints page http://www.ks.uiuc.edu/Research/namd/2.9/ug/node27.html , it says In all cases <atom> is a zero-based atom index , so the atom number should be one less than the pdb file should be given since in pdb file it starts from 1.
any input on this will be much appreciated.
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