Please keep this on the mailing list.
You need to minimise your structure to remove the large vdW
interactions you have at step 0 probably because of close waters in
the setup step. I still think you need to switch on SHAKE for the
water model you are using. Also consider a NPT run before production
to adjust the density.
&cntrl
imin = 1, ntmin = 2, maxcyc = 100, ncyc = 20,
ntwe = 100, ntpr = 10, ntwr = 100,
ntc = 2, ntf = 1,
noshakemask = ':L0,L1',
icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
timask1 = ':1', timask2 = ':2',
ifsc=1,
scmask1=':1XJ.C4,C5,C14,C15,C17,C24,C25,C26,C28,C29,C30,C37,C38,C39,C40,C41,C42,C47,N49,O58,S63,Cl6,F59,F60,F61,H4,H5,H14,H15,H49,H281,H282,H291,H292,H301,H302,H371,H372,H381,H382,H401,H402,H403,H411,H412,H413,H421,H422',
scmask2=':1X3.N1,N93,O1,C81,C82,C83,C4,C5,C86,C87,C88,C89,C90,H35,H36,H81,H82,H83,H4,H5,H86,H87,H88,H89',
crgmask='',
/
On Fri, 27 Jan 2017 11:46:24 +0000
Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> wrote:
> Hi Hannes,
>
> Here is the complete set up. You can try running at clambda = 1.
>
>
> I produce the ligands.parm7 and starting.rst7 files in the following
> way:
>
> tleap
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip4pew
> loadamberparams frcmod.tip4pewOn Fri, 27 Jan 2017 11:46:24 +0000
Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> wrote:
> Hi Hannes,
>
> Here is the complete set up. You can try running at clambda = 1.
>
>
> I produce the ligands.parm7 and starting.rst7 files in the following
> way:
>
> tleap
> source leaprc.ff14SB
> source leaprc.gaff
> loadamberparams frcmod.ionsjc_tip4pew
> loadamberparams frcmod.tip4pew
> loadoff 1XJ.lib
> loadamberparams 1XJ.frcmod
> loadoff 1X3.lib
> loadamberparams 1X3.frcmod
>
> WAT=TP4
>
> pling=loadpdb "LIG_INP-0.pdb"
> setbox pling centers
> saveamberparm pling ligands.parm7 starting.rst7
>
> quit
>
> Heating:
>
> mpirun -np 2 pmemd.MPI -i heat.in -c start.rst7 -ref start.rst7 -p
> ligands.parm7 -O -o heat.out -inf heat.info -e heat.en - heat.rst7 -x
> heat.nc -l heat.log
>
> The input file:
>
> heating
> &cntrl
> imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.001,
> ntt = 1, temp0 = 300.0, tempi = 50.0, tautp = 1.0,
> ntc = 1, ntf = 1,
> ntb = 1,
> ioutfm = 1, iwrap = 1,
> ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
> icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':1', timask2 = ':2',
> ifsc=1,
> scmask1=':1XJ.C4,C5,C14,C15,C17,C24,C25,C26,C28,C29,C30,C37,C38,C39,C40,C41,C42,C47,N49,O58,S63,Cl6,F59,F60,F61,H4,H5,H14,H15,H49,H281,H282,H291,H292,H301,H302,H371,H372,H381,H382,H401,H402,H403,H411,H412,H413,H421,H422',
> scmask2=':1X3.N1,N93,O1,C81,C82,C83,C4,C5,C86,C87,C88,C89,C90,H35,H36,H81,H82,H83,H4,H5,H86,H87,H88,H89',
> crgmask='',
> /
>
> &ewald
> /
>
> &wt
> type='TEMP0',
> istep1 = 0, istep2 = 8000,
> value1 = 50.0, value2 = 300.0
> /
>
> &wt type = 'END'
> /
>
> Production TI command:
>
> mpirun -np 2 pmemd.MPI -i ti.in -c heat.rst7 -p ligands.parm7 -O -o
> ti001.out -inf ti001.info -e ti001.en -r ti001.rst -x ti001.nc -l
> ti001.log
>
> The input file:
>
> TI simulation
> &cntrl
> loadoff 1XJ.lib
> loadamberparams 1XJ.frcmod
> loadoff 1X3.lib
> loadamberparams 1X3.frcmod
>
> WAT=TP4
>
> pling=loadpdb "LIG_INP-0.pdb"
> setbox pling centers
> saveamberparm pling ligands.parm7 starting.rst7
>
> quit
>
> Heating:
>
> mpirun -np 2 pmemd.MPI -i heat.in -c start.rst7 -ref start.rst7 -p
> ligands.parm7 -O -o heat.out -inf heat.info -e heat.en - heat.rst7 -x
> heat.nc -l heat.log
>
> The input file:
>
> heating
> &cntrl
> imin = 0, nstlim = 10000, irest = 0, ntx = 1, dt = 0.001,
> ntt = 1, temp0 = 300.0, tempi = 50.0, tautp = 1.0,
> ntc = 1, ntf = 1,
> ntb = 1,
> ioutfm = 1, iwrap = 1,
> ntwe = 1000, ntwx = 1000, ntpr = 1000, ntwr = 5000,
> icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 0,
> timask1 = ':1', timask2 = ':2',
> ifsc=1,
> scmask1=':1XJ.C4,C5,C14,C15,C17,C24,C25,C26,C28,C29,C30,C37,C38,C39,C40,C41,C42,C47,N49,O58,S63,Cl6,F59,F60,F61,H4,H5,H14,H15,H49,H281,H282,H291,H292,H301,H302,H371,H372,H381,H382,H401,H402,H403,H411,H412,H413,H421,H422',
> scmask2=':1X3.N1,N93,O1,C81,C82,C83,C4,C5,C86,C87,C88,C89,C90,H35,H36,H81,H82,H83,H4,H5,H86,H87,H88,H89',
> crgmask='',
> /
>
> &ewald
> /
>
> &wt
> type='TEMP0',
> istep1 = 0, istep2 = 8000,
> value1 = 50.0, value2 = 300.0
> /
>
> &wt type = 'END'
> /
>
> Production TI command:
>
> mpirun -np 2 pmemd.MPI -i ti.in -c heat.rst7 -p ligands.parm7 -O -o
> ti001.out -inf ti001.info -e ti001.en -r ti001.rst -x ti001.nc -l
> ti001.log
>
> The input file:
>
> TI simulation
> &cntrl
> imin = 0, nstlim = 100000, irest = 0, ntx = 1, dt = 0.001,
> ntt = 3, temp0 = 300.0, gamma_ln = 2.0, ig = -1,
> ntc = 1, ntf = 1,
> ntb = 2,
> ntp = 1, pres0 = 1.0, taup = 2.0,
> ioutfm = 1, iwrap = 1,
> ntwe = 100, ntwx = 100, ntpr = 100, ntwr = 100,
>
> icfe = 1, clambda = 1.0, scalpha = 0.5, scbeta = 12.0,
> logdvdl = 1,
> ifmbar = 1, bar_intervall = 1000, bar_l_min = 0.0, bar_l_max = 1.0,
> bar_l_incr = 0.1,
> timask1 = ':1', timask2 = ':2',
> ifsc=1,
> scmask1=':1XJ.C4,C5,C14,C15,C17,C24,C25,C26,C28,C29,C30,C37,C38,C39,C40,C41,C42,C47,N49,O58,S63,Cl6,F59,F60,F61,H4,H5,H14,H15,H49,H281,H282,H291,H292,H301,H302,H371,H372,H381,H382,H401,H402,H403,H411,H412,H413,H421,H422',
> scmask2=':1X3.N1,N93,O1,C81,C82,C83,C4,C5,C86,C87,C88,C89,C90,H35,H36,H81,H82,H83,H4,H5,H86,H87,H88,H89',
> crgmask=''
> /
>
> &ewald
> /
>
> Any help would be immensely appreciated.
>
> Sincerely,
>
> Stef
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Received on Fri Jan 27 2017 - 06:30:02 PST
