Difference between revisions of "Global optimization of biomolecules using AMBER9 with Structural Restraints"
import>Mp466 |
import>Mp466 |
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1. ''coords.inpcrd'' -- file with coordinates |
1. ''coords.inpcrd'' -- file with coordinates |
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− | 1.5 copy ''coords.inpcrd'' to ''refc'' where refc are the reference |
+ | 1.5 copy ''coords.inpcrd'' to ''refc'' where refc are the reference coordinates for the constraining potential |
2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here]) |
2. ''coords.prmtop'' -- topology file (see [http://wwmm.ch.cam.ac.uk/wikis/cuc3/index.php/Perm-prmtop.py here]) |
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− | 4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, where ntr=1,restraint_wt=500.0 determines the constraints and their |
+ | 4. ''min_md.in'' -- this file controls conditions for molecular dynamics in AMBER9, where ntr=1,restraint_wt=500.0 determines the constraints and their strength and restraintmask=':1-63' determines the residues affected. e.g.: |
STOP |
STOP |
Revision as of 12:22, 26 June 2008
This if similar to running plain global energy optimisation. Here you can find examples of input files necessary to work with GMIN:
1. coords.inpcrd -- file with coordinates
1.5 copy coords.inpcrd to refc where refc are the reference coordinates for the constraining potential
2. coords.prmtop -- topology file (see here)
3. min.in -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system, however in this particular case AMBER9 calculates only energy of the system, e.g.:
Minimization &cntrl imin=1, maxcyc=1, ncyc=1, igb=2, saltcon=0.2, ntx=1, ntb=0, cut=999.0 /
4. min_md.in -- this file controls conditions for molecular dynamics in AMBER9, where ntr=1,restraint_wt=500.0 determines the constraints and their strength and restraintmask=':1-63' determines the residues affected. e.g.:
STOP &cntrl imin = 0, tempi = 300.0, temp0 = 500.0, ntt = 3, gamma_ln = 1.0, nstlim = 300, dt = 0.001, igb = 2, saltcon = 0.1, ntb = 0, ntpr = 50, ntwx = 10,nrespa=1, cut = 10.0,rgbmax=8.22 ifswitch = 1 ntr=1,restraint_wt=500.0 restraintmask=':1-63' /
5. data -- file with GMIN keywords:
SLOPPYCONV 1.0D-6 TIGHTCONV 1.0D-7 MAXERISE 1.0D-4 MAXIT 100 600 MAXBFGS 1.0 DUMPSTRUCTURES SAVE 100 STEPS 1000 STEP 0.0 RADIUS 300 AMBERMDSTEPS AMBER9 coords.inpcrd inpcrd