On 2015-02-16 09:15, Pragya Priyadarshini wrote:
I have gone through previous archived mail and got the answer. We have
to load the ion parameter file it is not loaded by default..
Thanking you
Pragya.
> 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
--
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 Mon Feb 16 2015 - 00:00:02 PST
