Re: [AMBER] set command and VMD

From: Jason Swails <>
Date: Sat, 14 Mar 2015 21:16:02 -0400

On Sat, Mar 14, 2015 at 6:44 PM, Arjun Sharma <>

> Dear Amber users,
> 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.

​The method of visualization matters. Are you looking at a PDB file? Or
are you loading the prmtop file directly in VMD? If you're using the PDB
file, VMD draws bonds based on distance -- it has nothing to do with what
tleap assigns. Note that in this case, just because no bond is shown by
VMD does not mean it's not there. The inverse is also true -- just because
a bond *is* shown does not mean it *is* there.

If you want to see if a bond is defined in a topology file, your best bet
is to use the "printBonds" command in ParmEd to have a look.

> e.g.
> When I try to visualize the bond between say atom 1 and atom 4 of the
> fragment in VMD, I specify "index 1 4" but I see the bond between the next
> atoms (between atom 2 and atom 5 ), so to visualize the bond between atom 1
> and atom 4, I have to "index 0 3”. Why is that happening ?

​Either you're using a file that doesn't store bond information (like the
PDB file), or the bond is not getting defined by tleap. There's no way to
know based on the information you provided.

> ​​
> 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

​This suggests that POLB does not have an atom named "C1" in its second
residue. I suggest using the "desc" command, which will allow you to
inspect the contents of units, residues, and atoms.

For instance:

desc POLB

should tell you how many (and which) residues are in the unit. If there is
a second residue, then

desc POLB.2

should list all of the atoms within that residue. Etc. I suggest using
these introspection commands to try and determine why you are seeing the
errors you are seeing. It should also tell you if the head or tail atoms
of a particular unit are defined (and what they are).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sat Mar 14 2015 - 18:30:05 PDT
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