From: Axel Kohlmeyer (
Date: Tue Dec 15 2009 - 09:34:12 CST

On Tue, Dec 15, 2009 at 8:15 AM, Joshua Adelman <> wrote:
> Hi Leila,
> VMD usually just makes some guess about bonding from it's limited knowledge of amino/nucleic acid topology. If you have some non-standard molecules in you pdb files, it may not know how to handle them correctly.

actually, if you provide a .pdb file, the guess in VMD is based on
distances and
atom radii inferred from the atom names (assuming elements C, N, H, O
for _anything_
that starts with these letters).

> If you provide more information, someone might be able to give a more specific answer. For examples, when you load the initial and final structures into VMD before superposition with trjconv, do they display correctly? If so, you could alternatively superimpose the structures in VMD and see if that changes things.

the best way to preserve the bonding information is to load a topology
file (e.g. .psf) first
and then the coordinates on top of that. if you need to merge multiple
structures, there are
scripts for that, too.


> Best wishes,
> Josh
> On Dec 15, 2009, at 1:21 AM, leila karami wrote:
>> Hi
>> I used commands trjconv and trjcat for fitting and obtaining of superimposed structure between initial and final structure but when I open pdb file containing superimposed structure with VMD, 2 structure were shown but there is some exessive bonds.
>> please guide me.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.