My protein has 1466 atoms. My input file 2-9.nab is shown belowฃบ
*******************************************************************************
molecule m;
float xyz[4000],fret;
file file1;
file1=fopen("outx", "w" );
m = getpdb ("1h22_10.pdb");
readparm(m,"1h22_10.prmtop");
mm_options( "cut=999., ntpr=10, nsnb=99999, diel=C, gb=0 , dielc=4.0 ,wcons=200.0,maxarcdot=1500" );
setxyz_from_mol( m, NULL, xyz );
mme_init( m, "::H*", "::!.H=", xyz, file1);
// conjugate gradient minimization
conjgrad(xyz, 3*m.natoms, fret, mme, 0.00001, 0.000001, 1000 );
// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
newton( xyz, 3*m.natoms, fret, mme, mme2, 0.00000001, 0.0, 20 );
setmol_from_xyz( m,NULL, xyz );
putpdb("1h22_10_md.pdb",m);
// get the normal modes:
nmode( xyz, 3*m.natoms, mme2, 10, 0, 0.0, 0.0, 0);
fclose(file1);
*********************************************************************************************
The command to run the file is กฏnab 2_9.nabกฎ.
The prmtop fileobtained by the Amber.
At 2018-01-23 21:26:46, "David A Case" <david.case.rutgers.edu> wrote:
>On Tue, Jan 23, 2018, นฎรฮัฉ wrote:
>
>> When I used the Newton-Raphson method to optimize the protein, I got the following error ฃบ
>> กมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกมกม
>> Reading parm file (1h22_10.prmtop)
>> title:
>> default_name
>> Parameter topology includes 10-12 terms:
>> These are assumed to be zero here (e.g. from TIP3P water)
>
>This is unusual: do you know why you have 10-12 terms in the prmtop file?
>How did you create this file?
>
>> The reason for the optimization failure is not known because the
>> optimized protein is too large or not enough memory.
>
>How many atoms are in your simulation? The Newton-Raphson method takes *lots*
>of memory, which you might not have.
>
>Note that it is rarely necessary to use this method: if you are patient, xmin
>minimization can take you to a very low gradient, and requires much less
>memory.
>
>....dac
>
>
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Received on Fri Jan 26 2018 - 02:00:02 PST
