[AMBER] Problem with AMP atom separating in equilibration

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Mon, 7 Jan 2019 21:13:57 +0000

Dear Amber Users,

I am trying to run an RNA stem-loop with AMP as a ligand (from PDB: 1RAW).
AMP from that PDB structure had a net charge of -1 and a phosphate group
with the atom names:

ATOM 1167 OP1 AMP 37 40.698 22.533 20.524 1.00 0.00 O
ATOM 1168 P AMP 37 41.589 23.618 19.873 1.00 0.00 P
ATOM 1169 OP2 AMP 37 41.644 24.194 18.408 1.00 0.00 O
ATOM 1170 O3P AMP 37 42.456 22.359 19.560 1.00 0.00 O
ATOM 1171 HOP3 AMP 37 43.304 21.630 22.852 1.00 0.00 H

I did not find PREP and FRCMOD files for it at large, and so I ran antechamber and did not see
ant errors or warnings. However, in an unrestrained heating phase of equilibration
the run fails (Amber 18) and the final state PDB file shows the above HOP3 separated from
its O3P by 3.48A (starts at 0.99A atom center to atom center). The partial charge calculated
for this Hydrogen is very close to others at 0.429000, and LEAP sees the AMPs net charge
as -0.998. The whole RNA + AMP system is neutralized with Na+ ions and extra NaCl salt is
added to 0.15M concentration.

How should approach debugging this? I have never seen this kind of situation.

Thank you for any suggestions.
Best regards,
Voytek Kasprzak

Wojciech (Voytek) K. Kasprzak (Contractor)
Bioinformatics Analyst
Basic Science Program
Frederick National Laboratory for Cancer Research
Leidos Biomedical Research, Inc.
Post Office Box B
Frederick, Maryland 21702
Phone: 301-846-5537
AMBER mailing list
Received on Mon Jan 07 2019 - 13:30:02 PST
Custom Search