AMBER Archive (2008)

Subject: AMBER: Question about loading frcmod.ionsjc_tip3p in xleap

From: Jeff Schwinefus (schwinef_at_stolaf.edu)
Date: Wed Jul 09 2008 - 16:27:46 CDT

Hello
I apologize if this is a trivial question, but my searches in the
reflector archive have provided no insights. I am using AMBER 9 and I
have installed the updated DNA_CI.lib, ions08.lib, frcmod.parmbsc0, and
frcmod.ionsjc_tip3p files into the lib and parm subdirectories. My
command sequence in xleap to load these new libraries and parameters is:

>loadoff DNA_CI.lib
>loadoff ions08.lib
>mods = loadamberparams frcmod.parmbsc0
>mods2 = loadamberparams frcmod.ionsjc_tip3p

However, when I checked leap.log, I noticed that all monovalent cations
and anions are listed as UNKNOWN ATOM TYPE. This flag is a bit
disconcerting to me. Will AMBER actually use the LJ parameters from
frcmod.ionsjc_tip3p when I use the command addIons in xleap to add Na+
and Cl- ions to a DNA dodecamer (after solvating with tip3p water and
creating the .inpcrd and .prmtop files, of course)?

The section of leap.log associated with these commands is below. Thanks
for your help.

Jeff Schwinefus

leap.log
> loadoff DNA_CI.lib
Loading library: /home/apps/amber9/dat/leap/lib/DNA_CI.lib
Loading: DA
Loading: DA3
Loading: DA5
Loading: DC
Loading: DC3
Loading: DC5
Loading: DG
Loading: DG3
Loading: DG5
Loading: DT
Loading: DT3
Loading: DT5
> loadoff ions08.lib
Loading library: /home/apps/amber9/dat/leap/lib/ions08.lib
Loading: Br-
Loading: Cl-
Loading: Cs+
Loading: F-
Loading: I-
Loading: K+
Loading: Li+
Loading: Mg+
Loading: Na+
Loading: Rb+
> mods = loadamberparams frcmod.parmbsc0
Loading parameters: /home/apps/amber9/dat/leap/parm/frcmod.parmbsc0
Reading force field modification type file (frcmod)
Reading title:
modifies parm99 for nucleic acids: see http://mmb.pcb.ub.es/PARMBSC0/
> mods2 = loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /home/apps/amber9/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung &
Cheatham JPCB (2008)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> desc mods2
PARMSET
--Atoms
    Li+ Mass= 6.94 Polar= 0.03 E = 0.03 R= 1.02
          Element=? Hybrid= Sp0 Desc:
    Na+ Mass= 22.99 Polar= 0.25 E = 0.09 R= 1.37
          Element=? Hybrid= Sp0 Desc:
     K+ Mass= 39.10 Polar= 1.06 E = 0.19 R= 1.71
          Element=? Hybrid= Sp0 Desc:
    Rb+ Mass= 85.47 Polar=def=0 E = 0.33 R= 1.81
          Element=? Hybrid= Sp0 Desc:
    Cs+ Mass= 132.91 Polar=def=0 E = 0.41 R= 1.98
          Element=? Hybrid= Sp0 Desc:
     F- Mass= 19.00 Polar= 0.32 E = 0.00 R= 2.30
          Element=? Hybrid= Sp0 Desc:
    Cl- Mass= 35.45 Polar= 1.91 E = 0.04 R= 2.51
          Element=? Hybrid= Sp0 Desc:
    Br- Mass= 79.90 Polar= 2.88 E = 0.06 R= 2.61
          Element=? Hybrid= Sp0 Desc:
     I- Mass= 126.90 Polar= 4.69 E = 0.05 R= 2.86
          Element=? Hybrid= Sp0 Desc:
--Bonds
 --None
--Angles
 --None
--Torsions
 --None
--Impropers
 --None
--HBonds
 --None

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