Hi Hannes,
The previous e-mail was too big to post on the mailing list; it wouldn't let me.
Hmmm, the minimization seems to be doing the trick, although there aren't any clashes in my starting structures. Also, at lamda = 1 BOTH ligands would become completely distorted although at that lambda value the template isn't interacting with its environment at all. Also, even if there were clashes between the modeled ligand and any water molecules and/or ions, it wouldn't cause the whole molecule to become completely distorted and keep twisting and deforming throughout the whole run, let alone affect the template ligand at lambda = 1.
I've run 2000 steps of minimization on similar structures and I've had similar problems so I'm not sure if this is a general solution or works just in this particular case. I'm not really sure what's going on here.
In any event, thank you so much for your time and help. They are greatly appreciated.
Kind regards,
Stefan
________________________________________
From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
Sent: Friday, January 27, 2017 2:04 PM
To: amber.ambermd.org
Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd
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 - 07:00:04 PST
