On Fri, Mar 24, 2017, 巩梦雪 wrote:
> I think I hace done Newton-Raphson minimization to protein. However,
> I don't know how to get the optimized coordinates and output to a pdb
> file. Also I need to get a restart file for my next calculation. Here
> is the input lines.
You have already written a pdb file:
> putpdb("3jvs.min.pdb",xyz);
You can read this in again for your next calculation, but understand that
precision in PDB files is limited to 0.001 Ang. Use the putxv() routine
if you want higher precision in the output.
Note that your minimization failed! You need to run many more congjugate
gradient steps before starting newton-raphson minimization. Be sure to study
the outputs carefully and don't be afraid to experiment. Getting protein
normal modes is expensive, but things should usually work. 3jvs is a very
large protein: I'd suggest learning how things are done on much smaller
systems, and work your way up to bigger systems after that.
...good luck...dac
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Received on Fri Mar 24 2017 - 07:30:03 PDT
