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