Hi Lizelle,
First kindly try to autoimage your trajectory.
trajin*.crd
autoimage
trajout*.crd
I think this might fix it.
with regards,
-AT
________________________________
From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Sent: Thursday, October 19, 2017 1:44:48 AM
To: amber.ambermd.org
Subject: [AMBER] Protein drift from solvent box
Dear Amber users,
I have solvated my glycoprotein using the tleap input file given below. It specified that the distance between solute and boundary should be 10.0 and, assuming that this was the case, I proceeded to use this as input for MD.
Before minimization I ran this in cpptraj:
trajin protein.rst7
center
trajout protein_c.rst7
Minimization, heating, equilibration and production was then run starting from this centered structure. After looking at the production output, however, I am uncertain if this was correct. I see the protein moving out of the periodic box and thus tried to image it in cpptraj as follows:
parm protein.prmtop
trajin production.nc
center !:WAT,Na+ mass
go
image center !:WAT,Na+
go
trajout production_centered.nc
go
quit
Unfortunately, when viewing this trajectory in VMD the protein still sits outside the box.
I went back to the original protein_c.rst7 used as minimization input and noticed some glycan atoms seem to be right at the solvent border. Is there any way that I can verify if tLeap indeed kept a 10A boundary between the solute and solvent border? I am worried that the glycans interacted with the neighbouring periodic box. Could this be why the imaging doesn't work or am I doing it wrong?
Is it wrong to have iwrap=1 in the minimization input file?
tleap input:
########### Set Defaults ###################################################
set default PBRadii mbondi2
############################################################################
########### Force Field Inputs #############################################
source /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.ff14SB
source /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.GLYCAM_06j-1
source /apps/chpc/chem/amber/14/dat/leap/cmd/leaprc.gaff
addAtomTypes {
{ "NK" "N" "sp2" }
{ "NN" "N" "sp2" }
{ "ON" "O" "sp3" }
{ "Z1" "Zn" "sp3" }
{ "OK" "O" "sp3" }
}
loadoff HIT.lib
loadoff HIR.lib
loadoff WAR.lib
loadoff GLR.lib
loadoff ZN1.lib
loadamberparams ZN_reformat.frcmod
loadamberparams frcmod.ionsjc_tip3p
loadoff atomic_ions.lib
##########load Carb################
mol=loadpdb protein_RENUM.pdb
##########BONDING##################
bond mol.375.OE1 mol.662.Zn
bond mol.347.NE2 mol.662.Zn
bond mol.351.NE2 mol.662.Zn
bond mol.116.SG mol.122.SG
bond mol.316.SG mol.334.SG
bond mol.502.SG mol.514.SG
bond mol.36.ND2 mol.650.C1
.... rest of glycan bonding info....
############From#leapBOT##########
saveamberparm mol protein.prmtop protein.rst7
savepdb mol protein.pdb
#############Addions##############
addIons mol Na+ 0
addIons mol Cl- 0
saveamberparm mol protein_Neut.prmtop protein_Neut.rst7
savepdb mol protein_Neut.pdb
#############Solvate##############
solvateoct mol TIP3PBOX 10.0 1.0 iso
saveamberparm mol protein_Neut_Sol.prmtop protein_Neut_Sol.rst7
savepdb mol protein_Neut_Sol.pdb
quit
minimization input:
Constant Volume Minimization 1 of solvent
# Control section
&cntrl
imin=1,
irest = 0,
ntmin = 1, maxcyc = 5000, ncyc = 2500, dx0 = 0.01, drms = 0.0001,
cut = 10.0,
ntb = 1,
ntp = 0,
ntwx = 50,
ntpr = 50,
ntwr = 5000,
ioutfm = 1,
iwrap = 1,
ntr = 1, restraintmask='!:WAT,Na+', restraint_wt=50.0,
nmropt = 1,
/
&wt type = 'END'/
DISANG = protein_rnb.RST
/
in min.sh file:
exe=sander.MPI
mpirun -np 48 -machinefile $PBS_NODEFILE $exe -O -i min1.in -o min1.out -p protein_Neut_Sol.prmtop -c protein_Neut_Sol_c.rst7 -r min1.rst7 -ref protein_Neut_Sol_c.rst7
popd
production input:
Dynamic Simulation with Constant Pressure
# Control section
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 2, ntp = 1, pres0 = 1.0, taup = 1.0,
cut = 10.0,
ntc = 2, ntf = 2,
temp0 = 300.0,
ntt = 3, gamma_ln = 2, ig = -1,
nstlim = 2500000, dt = 0.002,
ntwx = 5000, ntpr = 5000, ntwe = 5000, ntwr = -100000,
ioutfm = 1,
iwrap = 1,
ntr = 0,
ntwprt = 0,
nmropt = 1,
/
&wt type = 'END'/
DISANG =CDOM_rnb.RST
/
Kind regards
Lizelle Lubbe
PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
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Received on Thu Oct 19 2017 - 07:30:02 PDT
