Thanks a lot. It was my mistake, probably $AMBERHOME variable was not
set/updated correctly to the Amber14. Loading leaprc.ff14SB first assigns
all the atomtype correctly.
Thanks
Mish
On Fri, Apr 25, 2014 at 4:15 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Fri, 2014-04-25 at 15:40 +0100, mish wrote:
> > Dear all,
> >
> > Is there any tutorial or help to use frcmod.ionslrcm_hfe_tip3p in
> > AmberTools14. When I load it atom types for all the ions in this file
> are
> > unknown: eg :
> > > loadAmberParams frcmod.ionslrcm_hfe_tip3p
> > Loading parameters: /amber14/dat/leap/parm/frcmod.ionslrcm_hfe_tip3p
> > Reading force field modification type file (frcmod)
> > Reading title:
> > Divalent ion parameters(HFE set) for Particle Mesh Ewald and TIP3P water
> > model from Li, Roberts, Chakravorty and Merz (JCTC 2013, 9, 27
> > 33-2748)
> > (UNKNOWN ATOM TYPE: Be2+)
> > (UNKNOWN ATOM TYPE: Cu2+)
> > (UNKNOWN ATOM TYPE: Ni2+)
> > (UNKNOWN ATOM TYPE: Pt2+)
> > .
> > .
> > (UNKNOWN ATOM TYPE: Ca2+)
> > (UNKNOWN ATOM TYPE: Sn2+)
> >
> ---------------------------------------------------------------------------
> > What should be the series tleap commands to load these parameters, and
> what
> > should be name Atom name and Residue Name of the Ions (for example Be2+)
> in
> > pdb file ? It would be great if some can point me into documents about
> > using these parameters in Amber.
>
> What series did you use? You should load a force field first (like
> ff14SB):
>
> source leaprc.ff14SB
> loadAmberParams frcmod.ionslrcm_hfe_tip3p
>
>
> The first chapters of the manual should walk you through this process.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Mon Apr 28 2014 - 00:30:04 PDT
