Sorry for mention that, if you think the lib file has too much information, which is not easy to check.
The $AMBERHOME/dat/leap/lib/atomic_ions.cmd file contains
the concise information about the corresponding relationship between each metal ion's atom name
and atom type.
On Apr 25, 2014, at 11:08 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Apr 25 2014 - 08:30:04 PDT
