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 Fri Apr 25 2014 - 08:30:05 PDT
