Re: [AMBER] Terminal phosphates with RNA

From: Piia Bartos via AMBER <amber.ambermd.org>
Date: Wed, 1 Mar 2023 10:12:12 +0000

Dear Prof Case,

It seems that the hydrogen is causing the crashing by bumping into neighboring atoms. Here are the distances of it to the in the last few frames
P (https://www.dropbox.com/s/tjukkrl26p7hhol/dist-HOP3-P.png?dl=0)
and OP2 (https://www.dropbox.com/s/aebv2bsog6pia3t/dist-HOP3-OP2.png?dl=0)

Is there some way to fix the zero vdW parameters?

Best regards,
Piia

--
Piia Bartoš, Ph.D. (Pharmacy)
Project Researcher
University of Eastern Finland | UEF | School of Pharmacy
Kuopio Campus | Canthia
Yliopistonranta 1 C | P.O. BOX 1627 | 70211 Kuopio
+358 50 548 8376 | piia.bartos.uef.fi
-----Original Message-----
From: David A Case <david.case.rutgers.edu> 
Sent: tiistai 28. helmikuuta 2023 15.46
To: Piia Bartos <piia.bartos.uef.fi>
Subject: Re: [AMBER] Terminal phosphates with RNA
On Fri, Feb 24, 2023, Piia Bartos wrote:
>
>I have checked the bonds, and to me they seem fine (similar to the next nt).
OK...this seems a bit at odds with your previous statement that the oxygens moved away from the phosphorus, and that the whole unit moved away from the rest of the RNA.
I suspect you may be getting bad contacts between HOP3 and one of the other oxygens on the terminal phosphate.  This hydrogen probably has zero vdW parameters.  Save a trajectory that fails with a fairly small value of ntwx, then use cpptraj to plot distances from that hydrogen to nearby atoms.
...good luck....dac
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Received on Wed Mar 01 2023 - 02:30:02 PST