Re: [AMBER] help about TMD

From: David A Case <>
Date: Tue, 28 Aug 2012 09:19:25 -0400

On Tue, Aug 28, 2012, 燕燕朱 wrote:

> I want to run TMD (targeted molecular dynamics ) by sander . Both of my
> initial molecular and targeted molecular are membrance proteins . The
> following is my input file and output file, I don’t know what’s wrong with
> my input file . I also want to know can you help me explain the parameter
> of tgtrmsmask .I am looking for you replay and will be very grateful for
> your kindhearted.

You should move carefully step by step. It looks like you are trying to
equilibrate the system and run targetted MD at the same time. Try the

1. Make sure you can run ordinary dynamics. Turn off targeted dynamics,
set ntpr=1 and nstlim=50. Get your system equilibrated to 300K. (If you have
problems at this stage, then you have a much simpler debugging strategy.)

2. You input file sets ntr=1, with a very large restraint weight. For that
part of the protein, nothing will be able to move. This will probably need to
be changed.

3. Try very simple targeted MD runs once you have an equilibrated protein.
To get started, still set ntpr=1 and nstlim to some smallish value (say 100).
Use the simplest restraints you can think of and study the output carefully to
try to understand exactly what is going on.

4. Your output says "old style PARM file read". This is somewhat
troublesome. How did you construct your prmtop file?

5. Consider upgrading. You version of sander is 6.5 years old, and few
people on the list would still have access to this version of the code.

...good luck...dac

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Received on Tue Aug 28 2012 - 06:30:03 PDT
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