AMBER Archive (2009)

Subject: Re: [AMBER] (no subject)

From: David A. Case (
Date: Fri Jan 16 2009 - 13:10:33 CST

On Fri, Jan 16, 2009, Jenny Iskrenova wrote:
> I have the same problem. Although I start with a good structure. The
> structure was created and the geometry was optimized in Materials
> Studio. I load the good initial pdb file in LeAP and add ions. Then I
> create the inpcrd and prmtop files. When viewed with VMD, the
> structure in the inpcrd file is distorted -- some of the bonds are
> really stretched.

Something is really wrong at this step, and you will need to track it
down. Leap just uses the coordinates you give it. So if you load a
"good" pdb, but the resulting inpcrd coordinates are "bad", something
has gone wrong, and you should not go further with MD, etc.

It might be that the problem is the interface to VMD -- does VMD look
"good" with the "good initial pdb" file? You may have to actually
examine the atomic coordinates in the inpcrd file (use ambpdb to convert
to pdb) vs. those in the input file, to find out what is going on.

Do the simplest possible LEap run (no addions, no solvent, just make a
vaccum model). See if things are getting distorted. Be sure to look
carefully at any warnings LEaP gives (missing atoms, extra atoms, etc.).
It is certainly possible that leap doesn't understand the Materials
Studio pdb file, for example.


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