Hi
I am new to AMBER as i use NAMD for simulation. I am using NAMD trajectories to analyze MMPB(GB)SA in ambertools 20. For the purpose i converted following CHARMM files into amber format:
Complex (Protein+ligand without water) PDB and PSF files into prmtopReceptor ====
Ligand =====
Solvated (Protein+Ligand+water+ions) =====
using following command in PARMED
chamber -psf file.psf -crd file.pdb -top file.top -param file.prm -str file.str
In my receptor there is a nickle atom that i have already parametrized in PSF file.
by using command in the manual mentioned the analysis started normally bu as the GB calculations has started it gave this error:CalcError: file location/complex.prmtopwxiting: all file have been retained
when i checked the gb.mdout file it was ended in the following error in the atomic coordinate and velocity section
FATAL: NATOM mismatch in coord and topology
The MMPBSA.in file is as follow
Input file for running PB and GB in serial
&general
endframe=100, start frame= 95, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
Need guidance plz
Thanks in advance
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Received on Mon Sep 21 2020 - 04:00:02 PDT
