To run a simulation in order to obtain the frequencies, I am using the following minimisation :
molecule m;
int ier;
float m_xyz[dynamic], f_xyz[dynamic];
float dgrad, fret;
m = getpdb("new.pdb");
allocate m_xyz[3*m.natoms];
allocate f_xyz[3*m.natoms];
readparm(m, "box.prmtop");
mm_options("ntpr=50, nsnb=20, cut=10., diel=C, gb=1, maxitn= 50000, ntwrism= 50 ,verbose= 2");
mme_init(m, NULL, "::ZZZZ", m_xyz, NULL);
// conjugate gradient minimization
setxyz_from_mol( m, NULL, m_xyz );
ier = conjgrad(m_xyz, 3*m.natoms, fret, mme, 0.005, 0.001, 50000 );
// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
ier = newton( m_xyz, 3*m.natoms, fret, mme, mme2, 0.0000000001, 0.0, 6 );
// get the normal modes:
ier = nmode( m_xyz, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
Previously I did use the command getpdb_prm(), but as it did not work, I took getpdb(), advise indicated on the manual (Basic molecular mechanics routines).
After running the file from the NAB compilation I get a error
[stregone.Coloss freq]$ ./a.out
Reading parm file (box.prmtop)
title:
BBZ
mm_options: ntpr=50
mm_options: nsnb=20
mm_options: cut=10.
mm_options: diel=C
mm_options: gb=1
mm_options: maxitn= 50000
mm_options: ntwrism= 50
mm_options: verbose= 2
Error: gb>0 is incompatible with periodic boundary conditions.
Error: To use this method set IFBOX in the PRMTOP file to 0.
Error: See http://ambermd.org/formats.html
The pdf file that I am using already comes from a minimisation (sander), it means that prmtop file is working. The manual says that if one has problems with the prmtop file, one could create a new in leap. Therefore I did try to create the prmtop by the following script:
tleap -f leaprc.ff12SB -f act
act
> source leaprc.gaff
loadamberparams broben.frcmod
dibr = loadpdb new.pdb
check dibr
saveamberparm dibr box.prmtop box.inpcrd
quit
Unfortunately, I am not able to create it, due to error (see attached file).
Please, could someone give some advices regarding to the recommended boundary conditions. whatever I change doe not seem to work (ntpr, nsnb, cut).
On the other hand, maybe it is something wrong with the prmtop file (for example atomtype),
that allow that to run sander but not nab.
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- application/octet-stream attachment: leap.log
Received on Thu Aug 25 2016 - 03:30:03 PDT
