Re: [AMBER] OHE residue and crashing

From: Piia Kokkonen <piia.kokkonen.uef.fi>
Date: Wed, 13 May 2020 12:46:18 +0000

Hi again,

I went peeking around the lib folder, and started to wonder. This unit position of OHE looks a bit odd.

!entry.OHE.unit.positions table dbl x dbl y dbl z
 1.866026 1.500000 -1.166025E-06
 2.030781 1.595123 -0.940962

It seems to be the same for other RNA lib files, but I can't find any other atom positions defined with such accuracy. Could this have something to do with my issue?

Also, could I get short instructions how to "add the LJ parameters to the hydrogen"?

Cheers,
Piia

--
Piia Kokkonen, Ph.D. (Pharmacy)
University of Eastern Finland
School of Pharmacy
P.O. BOX 1627
70211 Kuopio
Finland
Phone: +358 50 548 8376
Email: piia.kokkonen.uef.fi
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, May 12, 2020 15:21
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] OHE residue and crashing
On Tue, May 12, 2020, Piia Kokkonen wrote:
>
>Should the monophosphate.lib be in the tleap libraries or do I need to
>download it from somewhere?
It's called terminal_monophophate.lib.  You can always browse through
available libraries by going to $AMBERHOME/dat/leap/lib and poking
around.
....dac
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Received on Wed May 13 2020 - 06:00:04 PDT