Re: [AMBER] problem with peptide simulations

From: David A Case <>
Date: Mon, 28 Mar 2011 16:04:33 -0400

On Mon, Mar 28, 2011, Hashem Taha wrote:
> I am trying to simulate a peptide with the following sequence:
> p = sequence { VAL PRO ILE VAL THR PTR ALA ALA NHE }

I tend to agree with Jason that the phosphotyrosine may be the problem,
especially if it is protonated(?). You could certainly quickly try a run with
Tyr in its place to see if this helps to isolate the problem. Visualizing the
peptide structure before and after the sharp spike in temperature may also
help to point you in the right direction.


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Received on Mon Mar 28 2011 - 13:30:04 PDT
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