Hi Mish,
Have you loaded the atomic_ions.lib before loading the frcmod.ionslrcm_hfe_tip3p file?
The lib file has the function to matching the PDB metal ion names with the atom type using in
the frcmod file. You can check it for the detail information.
All the best,
Pengfei
On Apr 25, 2014, at 10:40 AM, mish <smncbr.gmail.com> 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.
>
> Best Wises,
> Mish
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Received on Fri Apr 25 2014 - 08:30:02 PDT
