Difference between revisions of "Global optimization of biomolecules using AMBER9"

From CUC3
Jump to navigation Jump to search
import>Em427
 
import>Em427
Line 5: Line 5:
 
2. ''coords.prmtop'' -- topology file (see [[Link here]])
  
2. ''coords.prmtop'' -- topology file (see [[Link here]])
   
  +
3. ''min.in'' -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.:
−
3. ''min.in'' --
  
  +
  +
Minimization
  +
&cntrl
  +
imin=1, maxcyc=1, ncyc=1,
  +
igb=2, saltcon=0.2,
  +
ntx=1, ntb=0,
  +
cut=999.0
  +
/
  +
  +
4. ''min_cd.in'' -- this file controls conditions for molecular dynamics in AMBER9, e.g.:
  +
  +
STOP
  +
&cntrl
  +
imin = 0,
  +
tempi = 500.0, temp0 = 700.0,
  +
ntt = 3, gamma_ln = 1.0,
  +
nstlim = 300, dt = 0.001,
  +
igb = 2, saltcon = 0.2,
  +
ntb = 0,
  +
ntpr = 100, ntwx = 100, nrespa=1,
  +
cut = 999.0
  +
/

Revision as of 10:31, 1 May 2008

Here you can find examples of input files necessary to work with GMIN:

1. coords.inpcrd -- file with coordinates

2. coords.prmtop -- topology file (see Link here)

3. min.in -- file with AMBER9 keywords describing the conditions for AMBER minimization of the studied system (however, we state to have one cycle only), e.g.: 

 Minimization
 &cntrl
    imin=1, maxcyc=1, ncyc=1,
    igb=2, saltcon=0.2,
    ntx=1, ntb=0,
    cut=999.0
  /

4. min_cd.in -- this file controls conditions for molecular dynamics in AMBER9, e.g.: 

  STOP
   &cntrl
    imin = 0,
    tempi = 500.0, temp0 = 700.0,
    ntt = 3, gamma_ln = 1.0,
    nstlim = 300, dt = 0.001,
    igb = 2, saltcon = 0.2,
    ntb = 0,
    ntpr = 100, ntwx = 100, nrespa=1,
    cut = 999.0
  /
Retrieved from "http://wikis.ch.cam.ac.uk/cuc3/wiki/index.php?title=Global_optimization_of_biomolecules_using_AMBER9&oldid=2540"