On Mon, Jun 8, 2015 at 8:05 AM, Suchetana Gupta <tutulg.gmail.com> wrote:
> Dear AMBER Users
> I am trying to run LeaP for a metalloprotein. Cobalt 2+ is the metal
> involved. Here is the input of my leap.in file:
>
>
> source leaprc.ff99SB
> source leaprc.gaff
> loadoff atomic_ions.lib
> #i know I should add a frcmod file here with vdW parameters for Co
> ACHE = loadpdb cda_co.pdb
> savepdb ACHE cda_co_out.pdb
> saveAmberParm ACHE cda_co.top cda_co.crd
> quit
>
>
> The error that I am getting is
>
> Building topology.
> Building atom parameters.
> For atom: .R<CO 230>.A<CO 1> Could not find vdW (or other) parameters for
> type: Co2+
> Parameter file was not saved.
> Quit
>
> I use AMBER12.
> How do I go about solving it?
>
Upgrade to AmberTools 15 and load the parameter file
frcmod.ionslrcm_cm_tip3p
where you put:
#i know I should add a frcmod file here with vdW parameters for Co
Not able to locate vdW parameters for Co2+ anywhere. Can someone please
>
>
share?
>
These parameters are part of AmberTools 15.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jun 08 2015 - 08:00:02 PDT
