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
Parameter file was not saved.
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Received on Sun Sep 27 2015 - 21:30:03 PDT
