Hi,
I am using amber14 to minimize a modelled protein containing Fe2+. Which
forcefield should I use to load the parameter for Fe2+??
I am using FF12SB,it showed following error while saving the topology
and coordinate file. When I add ions it also showed error in finding vdW
(or other) parameters for type: Na+.
source leaprc.ff12SB
----- Source: /home/bvs/amber14/dat/leap/cmd/leaprc.ff12SB
----- Source of /home/bvs/amber14/dat/leap/cmd/leaprc.ff12SB done
Log file: ./leap.log
Loading parameters: /home/bvs/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/bvs/amber14/dat/leap/parm/frcmod.ff12SB
Reading force field modification type file (frcmod)
Reading title:
ff12SB protein backbone and sidechain parameters
Loading library: /home/bvs/amber14/dat/leap/lib/amino12.lib
Loading library: /home/bvs/amber14/dat/leap/lib/aminoct12.lib
Loading library: /home/bvs/amber14/dat/leap/lib/aminont12.lib
Loading library: /home/bvs/amber14/dat/leap/lib/nucleic12.lib
Loading library: /home/bvs/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /home/bvs/amber14/dat/leap/lib/solvents.lib
> PDF=loadpdb spdffe.pdb
Loading PDB file: ./spdffe.pdb
total atoms in file: 1353
Leap added 1391 missing atoms according to residue templates:
1391 H / lone pairs
saveamberparm PDF pdf.top pdf.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<FE2 170>.A<FE2 1> Could not find vdW (or other) parameters
for type: Fe2+
Parameter file was not saved.
Please suggest the requisite to overcome this problem.
Thanking you,
--
Pragya Priyadarshini
PhD scholar
C/o Dr. Balvinder Singh
Bioinformatics Center (G N R P C)
Institute of Microbial Technology-CSIR
Sector 39A, Chandigarh-160036, INDIA
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Received on Sun Feb 15 2015 - 20:30:02 PST
