[AMBER] trajectory of minimization using generalized Born

From: Edwin Helbert Aponte Angarita <helbert2a.gmail.com>
Date: Wed, 18 Mar 2015 16:41:43 +0000

Dear All,

I am able to write the trajectory of a minimization of a peptide salvated
in TIP3PBOX. I have used this .in file


Then I calculate the rmsd to the first frame using ptraj and whith:
trajin ./min.mdcrd
rms first out rmsd_to_first.dat .N,CA,C

and I get a very nice plot showing how the peptide converges to a local
minimum and does not change noticeable any more. However, I cannot get
sander nor sander.MPI to write the trajectory file if I use generalized
Born implicit solvent. In that case I use:


and I am setting approppriatelly -i -o -p -c -r -x.

Do you know how can I get the trajectory when using generalized Born
implicit solvent? I only found a very old similar post (
http://archive.ambermd.org/200502/0076.html) but is not really helpful.


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Received on Wed Mar 18 2015 - 10:00:04 PDT
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