Hello, their,
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.
******************************************************************************************************************************
molecule m;
float xyz[4000], fret;
file file1;
file1=fopen("out.traj","w");
m = getpdb ("3jvs_wat_box.pdb");
readparm(m,"3jvs_wat_box.prmtop");
mm_options( "cut=999., ntpr=50, ntwx=1, nsnb=99999, diel=C, gb=1, dielc=1.0 , wcons=10000" );
setxyz_from_mol( m,NULL, xyz );
mme_init( m,"::H*" , "::!.H=", xyz, file1 );
// conjugate gradient minimization
conjgrad(xyz, 3*m.natoms, fret, mme, 0.1, 0.001, 200 );
// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
newton( xyz, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 50 );
setxyz_from_mol( m,NULL, xyz );
putpdb("3jvs.min.pdb",xyz);
// get the normal modes:
nmode( xyz, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
fclose(file1);
***********************************************************************************************************
command： nab test.nab
./a.out > test.out
The output and input files are in the attachment.
Any help?
Thanks!
At 2017-03-23 21:38:01, "David Case" <david.case.rutgers.edu> wrote:
>On Thu, Mar 23, 2017, 巩梦雪 wrote:
>
>> How to perform Newton-Raphson minimization to protein? I only found the
>> Newton-Raphson method in the NAB module which treats nucleic acid. I
>> am not sure if the Newton-Raphson minimization can , or not, used to
>> protein, and how ?
>
>In spite of its name, NAB is a general-purpose modeling program, and deal with
>any type of molecule that Amber supports (proteins, nucleic acids, lipids,
>carbohydates, etc.)
>
>....dac
>
>
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- application/octet-stream attachment: test.nab
- application/octet-stream attachment: test.out
- application/octet-stream attachment: out.traj
Received on Fri Mar 24 2017 - 07:00:03 PDT
