[AMBER] Problem with using the 12-6-4 LJ-Type Nonbonded Model in a an RNA-Mg system

From: Kasprzak, Wojciech (NIH/NCI) [C] <"Kasprzak,>
Date: Thu, 20 Aug 2015 20:08:09 +0000

Dear Amber Users,

I was able to repeat the tutorial on "Modeling a Magnesium-DNA System
using the 12-6-4 LJ-Type Nonbonded Model" using our Amber14 / ff14SB environment
(http://ambermd.org/tutorials/advanced/tutorial20/12_6_4.htm). It worked with the SPCE
(the tutorial case) and TIP3P water models.

However, when I attempted to use the same protocol with two different RNA molecules
(and the TIP3P waters) I run into fatal errors in each case at the level of parmed.py command.
In the middle of the list of atoms for which the C4 terms are being added the following errors appear,
each terminating the run for 2 separate RNA molecules, pre-minimized in Amber (GBSA)
and with MGs added in leap:

 Action add12_6_4 failed
    LJ12_6_4Error: Could not find parameters for ATOM_TYPE CS (RNA 1)
    LJ12_6_4Error: Could not find parameters for ATOM_TYPE C4 (RNA 2)

The biggest ATOM_TYPE_INDEX = 15, and the failure happens after 7 successful steps.

Does it look familiar to anybody? Does anyone have a working sample of leap and parmed
commands (input files) that have been successfully tested for the RNA? If you need
more information from me, please, let me know.

Hoping to get some help on this issue.
Best regards,
Voytek Kasprzak

Wojciech (Voytek) Kasprzak [Contractor]
Analyst Programmer,
Basic Science Program, Leidos Biomedical Research, Inc.
Frederick National Laboratory for Cancer Research, Frederick, MD.
(301) 846 5537
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Received on Thu Aug 20 2015 - 13:30:04 PDT
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