On Mon, Sep 28, 2015 at 12:29 AM, 杨川 <junaid.hust.edu.cn> wrote:
> Dear Amber Users
> I am using amber14 with Amber15 tools to simulate a complex having ligand
> and heme group. The heme group is attached to Cysteine residue. I used
> the following input file. What might be the solution?
>
> Thank you
>
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams lig.frcmod
> LIG = loadmol2 lig.mol2
> loadamberparams frcmod.hemall
> loadamberprep heme_all.in
> com = loadpdb clean.pdb
> saveamberparm com com.top com.crd
>
> I have got this error...
>
> > saveamberparm com com.top com.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -7.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 412>.A<NA 2> Could not find vdW (or other) parameters for
> type: NP
> For atom: .R<HEM 412>.A<NB 23> Could not find vdW (or other) parameters
> for type: NO
> For atom: .R<HEM 412>.A<NC 39> Could not find vdW (or other) parameters
> for type: NP
> For atom: .R<HEM 412>.A<ND 55> Could not find vdW (or other) parameters
> for type: NO
>
It looks like frcmod.hemall is missing some nonbonded parameters
(particularly for atom types NP and NO). You need to supply these
parameters for LEaP to work.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Sep 28 2015 - 05:30:03 PDT
