Hello,
I have been trying to perform an implicit solvent constant pH molecular dynamics simulation of an eleven residue polypeptide chain at pH = 5, but I have been having difficulties with performing the heating portion of the simulation. The problem that keeps happening is that the heating will end after a few seconds and no output files will be generated. I think the issue is either with my parameter and topology file or the .rst file that was produced during the initial minimization because I have attempted to use previous heating input files- which have worked in the past for other structures- and these files have also had the same issue. Below are the commands and input files I used to minimize the chain. Is there somewhere that I skipped a step or made an error in the input files? Thanks for all the help.
Thanks,
Chase Zagorec-Marks
Commands:
pdb4amber -i 11-mer_pH.pdb —constantph -o 11-mer_pH_2.pdb
xleap
source leaprc.constph
x = loadpdb 11-mer_pH_2.pdb
check x
This returned:
Checking 'x'....
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
Checking parameters for unit 'x'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 1
Unit is OK.
saveamberparm x 11-mer_pH.parm7 11-mer_pH.inpcrd
saveamberparm x 11-mer_pH.parm7 11-mer_pH.rst7
Note: When viewed in vmd the structure looked fine for .parm7 and .rst7, but when viewed in vmd the chain has the nitrogen of the n-terminal extending far from the rest of the chain for the .inpcrd file.
exit xleap
cpinutil.py -p 11_mer_pH.parm7 -resnames HIP GL4 AS4 -o 11_mer_pH.cpin
Min.in file:
Minimization of eleven mer for constant pH MD
&cntrl
imin = 1,
igb = 2,
saltcon = 0.1,
maxcyc = 10000,
ncyc = 1000,
icnstph = 1,
ntcnstph = 1000000,
cut = 1000.0,
ntr = 1,
restraint_wt = 10,
restraintmask = '.CA,C,O,N'
/
sander.MPI -O -i min.in -o min.mdout -p 11_mer_pH.parm7 -c 11_mer_pH.rst7 -ref 11_mer_pH.rst7 -r min.rst7 -cpin 11_mer_pH.cpin
Heat.in file:
Implicit solvent constant pH initial heating mdin
&cntrl
imin=0, irest=0, ntx=1,
ntpr=250, ntwx=250, nstlim=2000000,
dt=0.0005, ntt=3, tempi=10,
temp0=300, tautp=2, ig=-1,
ntp=0, ntc=2, ntf=2, cut = 999,
ntb=0, igb=2, tol=0.000001,
nrespa=1, saltcon=0.1, icnstph=1,
solvph=5, ntcnstph=100000000,
gamma_ln=5.0, ntwr=250, ioutfm=1,
nmropt=1, ntr=1, restraint_wt=1.0,
restraintmask='.CA,C,O,N',
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=1000000,
VALUE1=10.0, VALUE2=300.0,
/
&wt TYPE='END’ /
sander.MPI -O -i heat.in -o heat.mdout -p 11_mer_pH.parm7 -c min.rst7 -ref min.rst7 -r heat.rst7 -cpin 11_mer_pH.cpin -x heat.mdcrd
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Received on Thu Jan 26 2017 - 12:30:05 PST
