Re: [AMBER] Novice Question: MD Visualisation in VMD

From: Horn, Anselm <>
Date: Sun, 13 May 2018 12:07:40 +0000

Dear Billy,

just a short answer:
The prmtop file holds the information about atom identities, parameters and connectivity; the crd file (like the restart file) contains a single set of coordinates, augmented with a set of velocities (necessary for restarts); the mdcrd file contains several sets of coordinates, normally without velocities.

Now, VMD needs both, topology and coordinates to correctly display any structure; thus, you first have to load a prmtop file, in order to tell VMD abouth the atoms and residues of the system, and in a next step you load the pure coordinate files like mdcrd.

I hope this helps.



Von: Billy Williams-Noonan []
Gesendet: Sonntag, 13. Mai 2018 10:09
An: AMBER Mailing List
Betreff: [AMBER] Novice Question: MD Visualisation in VMD

Hi Experts,

I've been using GROMACS for the past two years. This past week I have been
learning to use Amber.

I want to visualise my MD trajectory in VMD and have been (loosely)
following this
tutorial on my system. I am simulating a tetramer with a ligand bound to
each monomeric unit.

When I load my file into VMD for the coordinates and add the
trajectory data (em.mdcrd or nvt.mdcrd), no frames load into the coordinate
file. Do I need a .prmtop file instead? I have been following the
instructions on the tutorial linked earlier.

My understanding that em.mdcrd is the trajectory for my energy minimisation
and nvt.mdcrd is my trajectory for my nvt run.

MD is being run with sander and we do not have access to pmemd yet.

Please advise? Let me know if further information is needed.


Billy Noonan*    |    *PhD Student    *|*    Bsci ( *Adv* ), IA Hon
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**|*   +61420 382 557
Monash Institute for Pharmaceutical Sciences ( *MIPS* )
Royal Parade, Parkville, 3052
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Received on Sun May 13 2018 - 05:30:02 PDT
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