Dear All,
I would like to carry out a target dynamics.
Following suggestion fro the mailing list
i have computed parameters for starting and reference conformations of
studied protein with leap,
checked the number of atoms and computed the minimization for both
conformations.
When i use sander to carry out target dynamics calculation the system
was frozen at the step 0 with the RMSD higher that the real one and with
CPU working at 100%.
I suppose that the problem could be the size of the water boxes for the
two protein conformations
but i do not know how to solve the problem
Do you have any suggestions?
My input file is:
&cntrl
nstlim= 10000000, dt=0.002, temp0=300.0, ntt=1,
ntpr=500, ntwr=5000, ntwx=5000,
ntx=1, ntpr=100,
ntf=1, ntc=1, ntb=0,
igb=1, gbsa=0,
nsnb=25,
itgtmd=1, tgtmdfrc=10,
tgtfitmask=":1-674.CA,N,C,O",
tgtrmsmask=":1-674.CA,N,C,O",
&end
&wt type='TGTRMSD', istep1=1, istep2=10000000, value1=2.00 , value2=0.0,
> &end
Any help will be really appreciated.
with best regards
Antonio
--
Antonio Coluccia, Ph.D.
Department of Chemistry and Drugs Tecnology
La Sapienza University
Rome 00185
Piazzale Aldo Moro 5
antonio.coluccia.uniroma1.it
mobile: 00393406113351
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Received on Mon Dec 22 2014 - 06:00:06 PST
