AMBER Archive (2006)

Subject: AMBER: protonated phosphate

From: Einar Uggerud (einar.uggerud_at_kjemi.uio.no)
Date: Tue Nov 28 2006 - 01:11:46 CST

Hello!

I am new to Amber, but learned a lot from reading
your excellent tutorials. I was particularily
thrilled by finding a web page
(http://amber.scripps.edu/antechamber/dna.html)
adressing the problems of protonated phosphate
groups, exactly what I was looking for. The
procedure is a bit difficult to understand,
however, and I have two questions.

1. Do you have copies of the .prepi files DA3P,
DC3P, DG3P and DT3P mentioned in the text. It is
very convenient that the DAP, DCP, DGP and DTP
actually are given at the page.

2. Where do I find and how do I prepare .ac files (mentioned in Step 5).

3. It seems difficult to mix non-protonated and
protonated units in the same molecule (see the
xleap session below). Do you have any advice?

Best regards, Einar Uggerud
-------------------------

> aa=sequence{DC5 DCP DC3}
> edit aa
> saveamberparm aa test.prmtop test.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.

  -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: P - O
Building angle parameters.
Could not find angle parameter: OS - P - O
Could not find angle parameter: O - P - OS
Could not find angle parameter: OH - P - O
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
  <DCP 2>: C5 H6 C6 N1
  <DCP 2>: C4 C6 C5 H5
  <DCP 2>: C5 N4 C4 N3
  <DCP 2>: N1 N3 C2 O2
  total 18 improper torsions applied
  4 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved. 

-- 
******
Professor Einar Uggerud
Kjemisk institutt
Universitetet i Oslo

einar.uggerud_at_kjemi.uio.no

http://www.kjemi.uio.no/ms

For the period 1. September 2006 - 15. July 2007
the following address is effective:
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Telephone (Dep.of Chemistry)	+49 (0) 6421 28 25686
Telephone (Private):		+49 (0) 6421 350255
(omit (0) when calling from outside Germany).
******
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