Re: restraints and constraints in NAMD

From: Vermaas, Joshua (
Date: Wed Feb 22 2017 - 11:57:14 CST

Hi Lara,

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:
Good evening
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 , 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.

Thank you

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