[AMBER] Implicit Solvent CpHMD

From: Chase Zagorec-Marks <chasezgrcmrks.gmail.com>
Date: Thu, 26 Jan 2017 13:29:21 -0700


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.

Chase Zagorec-Marks


pdb4amber -i 11-mer_pH.pdb —constantph -o 11-mer_pH_2.pdb


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
   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
   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,
   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
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