AMBER Archive (2008)

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

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu Jul 10 2008 - 17:20:04 CDT

> 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)?

Yes, this is disconcerting and gave me a momentary panic. The proof that
all appears OK is in the prmtop where you can check the resulting vdw
parameters to see if they indeed match expectations.

rdparm prmtop
printtypes

I looked through my leap.log(s) and see the same behavior, yet my prmtop
appears OK (i.e. printtypes shows radii/eps as expected). Perhaps DAC
will have a better explanation for the warning, but I think it is spurious...

> > loadoff ions08.lib
...
> (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-)

--tec3
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