Re: [AMBER] Cyana3.97 to Amber15 pdb conversion

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Wed, 3 Aug 2016 13:26:52 -0600

Hi,

We need some more information before we can help. Can you list the
exact steps you tried (i.e. commands, flags, input) and any relevant
output messages (warnings, errors, etc). Thanks,

-Dan

On Wed, Aug 3, 2016 at 9:09 AM, Erik Davis <erikd.g.clemson.edu> wrote:
> Dear all:
>
>
> We are attempting to refine NMR-derived structures of 9-bp DNA sequences.
> NMR ensembles employing NOE and torsion restraints were calculated using
> CYANA 3.97 energy minimization software. The DNA tutorial,
> http://ambermd.org/tutorials/basic/tutorial1/, was used for as the basis
> for our refinement protocol using Amber15 and Ambertools software. However,
> we have encountered issues when converting a CYANA pdb to an AMBER pdb.
>
>
> The problem essentially hinges on the ability to produce usable prmtop and
> inpcrd files for minimization. While we have successfully converted a cyana
> pdb to an amber compatible pdb from which the prmtop and inpcrd files were
> successfully generated without errors, the resulting refined pdb produces
> many bonding errors in the phosphate backbone as well as in between
> adjacent intra-strand bases and in some cases truncates the minimization
> entirely.
>
>
> Any help on this cyana to amber pdb conversion problem is greatly
> appreciated.
>
>
> Respectfully,
> ------------------------------
>
>
> --
> Erik V. Davis
> Clemson University
>
> 攀登山脉
> Pāndēng shānmài
>
> "Only one who attempts the absurd can achieve the impossible"
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-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Wed Aug 03 2016 - 12:30:03 PDT
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