Re: [AMBER] set command and VMD

From: David A Case <>
Date: Sun, 15 Mar 2015 20:45:43 -0400

On Sat, Mar 14, 2015, Arjun Sharma wrote:
> I’m trying to merge two polymer fragments into one. I use “set"
> command to specify head and tail of two fragments and use “bond” or
> “sequence” command to combine them. The problem is when I try to
> visualize this merged fragment in VMD, I see that for some reason VMD
> considers atom # 1 as atom # 0.

I don't think this has anything to do with Amber. VMD starts counting atoms
from 0, not from 1.

> My other question is when I use the “set command” in tleap as shown below
> >set POLA tail POLA.1.C1
> >set POLB head POLB.2.C1
> The value must be of the type: Atom
> Why can’t use the POLB fragment as residue 2 since it will be
> residue 2 in the merged fragment ? It works when I use "set POLB head
> POLB.1.C1”

The fact that POLB be "will be" residue 2 in some future molecule is not
relevant, (and there is no way that LEaP would know what you plan to do later
on.) As it stands, POLB has one residue, which is residue number 1.

The two issues you raise are not related, as far as I can see.


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Received on Sun Mar 15 2015 - 18:00:03 PDT
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