AMBER Archive (2002)

Subject: Re: About counterions

From: David A. Case (case_at_scripps.edu)
Date: Thu Dec 05 2002 - 13:47:04 CST

On Thu, Dec 05, 2002, Andrei Leitão wrote:
>
> I am doing some molecular dinamics from heptamers and I
> had problems with the end base pairs (only one part was
> very distorted - about 90 degrees). I think that
> counterions were important to the distortion because some
> of them were very far from the phosphate backbone.

Neither of these observations is unexpected: end base pairs sometimes "fray",
and counterions are not expected to stay close to phosphates.

Of course, there may indeed be problems with the simulation, but one cannot
tell from just this information alone.

> I have more one question: How can I change the mdcrd files
> to the pdb files? I did not find it on the manual.

ptraj or carnal can write out pdb files from trajectory ("mdcrd") files;
ambpdb can convert restart files into pdb.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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