Dear Prof Case,
I have checked the bonds, and to me they seem fine (similar to the next nt).
Here are the parmed outputs:
>printBonds :840 (OHE)
Atom 1 Atom 2 R eq Frc Cnst
13425 OP3 ( OH) 13426 P ( P) 1.6100 230.0000
13424 HOP3 ( HO) 13425 OP3 ( OH) 0.9600 553.0000
> printBonds :841 (C5')
Atom 1 Atom 2 R eq Frc Cnst
13425 OP3 ( OH) 13426 P ( P) 1.6100 230.0000
13455 O3' ( OS) 13456 P ( P) 1.6100 230.0000
13451 C2' ( CT) 13453 O2' ( OH) 1.4100 320.0000
13449 C3' ( CT) 13451 C2' ( CT) 1.5260 310.0000
13449 C3' ( CT) 13455 O3' ( OS) 1.4100 320.0000
13447 C2 ( C) 13448 O2 ( O) 1.2290 570.0000
13445 N3 ( NA) 13447 C2 ( C) 1.3880 418.0000
13443 C4 ( C) 13444 O4 ( O) 1.2290 570.0000
13443 C4 ( C) 13445 N3 ( NA) 1.3880 418.0000
13441 C5 ( CS) 13443 C4 ( C) 1.4440 410.0000
13439 C6 ( CS) 13441 C5 ( CS) 1.3500 549.0000
13438 N1 ( N*) 13439 C6 ( CS) 1.3650 448.0000
13438 N1 ( N*) 13447 C2 ( C) 1.3830 424.0000
13436 C1' ( CT) 13438 N1 ( N*) 1.4750 337.0000
13436 C1' ( CT) 13451 C2' ( CT) 1.5260 310.0000
13435 O4' ( OS) 13436 C1' ( CT) 1.4100 320.0000
13433 C4' ( CT) 13435 O4' ( OS) 1.4100 320.0000
13433 C4' ( CT) 13449 C3' ( CT) 1.5260 310.0000
13430 C5' ( CI) 13433 C4' ( CT) 1.5260 310.0000
13429 O5' ( OS) 13430 C5' ( CI) 1.4100 320.0000
13426 P ( P) 13427 OP1 ( O2) 1.4800 525.0000
13426 P ( P) 13428 OP2 ( O2) 1.4800 525.0000
13426 P ( P) 13429 O5' ( OS) 1.6100 230.0000
13453 O2' ( OH) 13454 HO2' ( HO) 0.9600 553.0000
13451 C2' ( CT) 13452 H2' ( H1) 1.0900 340.0000
13449 C3' ( CT) 13450 H3' ( H1) 1.0900 340.0000
13445 N3 ( NA) 13446 H3 ( H) 1.0100 434.0000
13441 C5 ( CS) 13442 H5 ( HA) 1.0800 367.0000
13439 C6 ( CS) 13440 H6 ( H4) 1.0800 367.0000
13436 C1' ( CT) 13437 H1' ( H2) 1.0900 340.0000
13433 C4' ( CT) 13434 H4' ( H1) 1.0900 340.0000
13430 C5' ( CI) 13431 H5' ( H1) 1.0900 340.0000
13430 C5' ( CI) 13432 H5'' ( H1) 1.0900 340.0000
Interestingly, I noticed that the system stays stable in the equilibration simulation, where I use the Berendsen barostat and a timestep of 2 fs. This can be extended as the production run for at least 150ns. Visually this simulation seems fine and the phosphates behave as expected. What I find a bit odd is that the simulation crashes like the previous ones if I try to use the 4fs timestep (I used HMR for the input files).
Can the parameters be so slightly off that a bit harsher simulation settings cause the phosphates to explode?
Cheers,
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: torstai 23. helmikuuta 2023 20.04
To: Piia Bartos <piia.bartos.uef.fi>
Subject: Re: [AMBER] Terminal phosphates with RNA
On Wed, Feb 22, 2023, Piia Bartos wrote:
>
>I have visualized the trajectories, and the issue is that the oxygens
>start to stretch away from the phosphate, and the phosphate also moves
>away from the rest of the RNA. This is usually visible on the last
>frame I can visualize in VMD without VMD crashing.
Something is clearly wrong (someplace) in the setup.
Use parmed to print out all the bonds in the first residue (printBonds :1).
Are there bonds between the P and O atoms where they should be?
....dac
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Received on Fri Feb 24 2023 - 03:30:02 PST
