AMBER Archive (2008)

Subject: AMBER: Regarding force field ff02 and ion library

From: Abhishek Singh (asingh7_at_ncsu.edu)
Date: Mon Jun 30 2008 - 15:54:52 CDT

 Dear All

I have a situation that, I work on Amber 9 (compiled on linux for parallel
computing on IBM p575). Regarding RNA molecule, I tried to use ff02 force
field and need to incorporate ion libraries "frcmod.ionsjc_tip3p". I am
unable to load new ion library. shown below is the xleap response "xleap -f
leaprc.rna.ff02" , also when I load parameters "frcmod.ff02pol.r1" it says
that backbone disabled? why would one like to do so. Kindly suggest

Welcome to LEaP!

(no leaprc in search path)

Sourcing: /usr/local/apps/amber9/dat/leap/cmd/leaprc.rna.ff02

Log file: ./leap.log

Loading parameters: /usr/local/apps/amber9/dat/leap/parm/parm99.dat

Reading title:

PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99

Loading library: /usr/local/apps/amber9/dat/leap/lib/all_nucleic02.lib

Loading library: /usr/local/apps/amber9/dat/leap/lib/all_amino02.lib

Loading library: /usr/local/apps/amber9/dat/leap/lib/all_aminoct02.lib

Loading library: /usr/local/apps/amber9/dat/leap/lib/all_aminont02.lib

Loading library: /usr/local/apps/amber9/dat/leap/lib/ions94.lib

Loading library: /usr/local/apps/amber9/dat/leap/lib/solvents.lib

> loadamberparams frcmod.ff02pol.r1

Loading parameters: /usr/local/apps/amber9/dat/leap/parm/frcmod.ff02pol.r1

Reading force field modification type file (frcmod)

Reading title:

DISABLE BACKBONE AND NO-HYDROGEN

> loadamberparams frcmod.ionsjc_tip3p

Could not open file frcmod.ionsjc_tip3p: not found

Abhishek Singh
North Carolina State University

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