Dear Amber User.
Thank you so much for the help.. I have added the parameters for the NP and NO to the bottom of the "frcmod.hemall" file.. And it work well .Now its look like this
NONBON
FE 1.20000 0.05000 0.00000
LO 1.60000 0.20000 0.00000
LC 1.85 0.12 0.0
NP 1.8240 0.1700 OPLS
NO 1.8240 0.1700 OPLS
-----Original Messages-----
From: "Ñî´¨" <junaid.hust.edu.cn>
Sent Time: Monday, September 28, 2015
To: amber.ambermd.org
Cc:
Subject: Problem with saving parameters for a complex having Heme group
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 Tue Sep 29 2015 - 20:30:03 PDT
