Hi
I was able to figure out why sander was not working.
I fixed it. I will now try to implement what Andy suggested, and see if
it helps.
I will update on what happens.
Thanks for the help.
Regards
On Tue, May 1, 2018 at 6:33 PM, Abhilash J <md.scfbio.gmail.com> wrote:
> Hi
>
> I tried xmin minimizer by setting ntmin=3. It turns out pmemd does not
> support ntmin=3. So i tried sander.MPI with ntmin=3 and 1. But somehow it
> throws error for the same input which pmemd runs fine.
> I think there is some format difference in input of sander and pmemd in
> case of input file which i am unable to point out. I have tried several
> different variations none yielded a positive result.
> Can you help me out in finding this difference.
>
>
>
> *The output says:* LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
> defa
> ----- READING GROUP 1; TITLE:
> simulated annealing protocol, 20 ps
>
> rfree: Error decoding variable 1 3 from:
> &cntrl
>
> this indicates that your input contains
>
> incorrect information
>
> field 1 was supposed to
>
> have a (1=character, 2=integer, 3=decimal) value
>
>
>
>
> *in file says:*simulated annealing protocol, 20 ps
> &cntrl
> imin=1, ntx=1, irest=0, ntpr=50, ntf=1, ntb=1, ntmin=3,
> cut=9.0, nsnb=10, ntr=1, maxcyc=5000, ncyc=2000, nmropt=1,
> /
> &wt type='REST', istep1=0,istep2=1500,value1=1.0, value2=1.0, /
> &wt type='REST', istep1=1501,istep2=5000,value1=1.0, value2=1.0, /
> &wt type='END' /
> LISTOUT=POUT
> DISANG=restraints
> &end
>
>
> * the restraints file reads as (as it has non bonded ion and water
> prepared through MCPB.py):*
>
>
> # Harmonic restraints for the restrained nonbonded model of comp
> &rst iat=453,6526, r1=0., r2=2.0741, r3=2.0741, r4=100., rk2=32.4000,
> rk3=32.4000,/
> &rst iat=6526,6534, r1=0., r2=2.0336, r3=2.0336, r4=100., rk2=44.2000,
> rk3=44.2000,/
> &rst iat=6526,6533, r1=0., r2=1.9882, r3=1.9882, r4=100., rk2=69.0000,
> rk3=69.0000,/
> &rst iat=6526,6538, r1=0., r2=2.1393, r3=2.1393, r4=100., rk2=30.6000,
> rk3=30.6000,/
> &rst iat=6526,6570, r1=0., r2=2.1012, r3=2.1012, r4=100., rk2=46.6000,
> rk3=46.6000,/
> &rst iat=6526,6573, r1=0., r2=2.1097, r3=2.1097, r4=100., rk2=43.8000,
> rk3=43.8000,/
> &rst iat=6529,6600, r1=0., r2=1.7272, r3=1.7272, r4=100., rk2=43.8000,
> rk3=43.8000,/
> &rst iat=392,6599, r1=0., r2=1.6389, r3=1.6389, r4=100., rk2=43.8000,
> rk3=43.8000,/
>
>
> On Tue, May 1, 2018 at 5:31 AM, Goetz, Andreas <agoetz.sdsc.edu> wrote:
>
>> Your problem is probably not related to QM/MM. Maybe try optimizing with
>> MM before attempting a QM/MM optimization. In this way your MM environment
>> is already relaxed and in a subsequent QM/MM optimization you should see
>> mostly changes in the QM region and around the QM/MM boundary. Also note
>> that the default optimizer in Amber is not very efficient and requires many
>> steps to converge. You can try the xmin optimizer (set ntmin = 3), which
>> provides algorithms that are quadratically convergent - these converge much
>> faster, but are still expensive due to repeated energy/force evaluations
>> during the line search.
>>
>> All the best,
>> Andy
>>
>> —
>> Dr. Andreas W. Goetz
>> Assistant Research Scientist
>> San Diego Supercomputer Center
>> Tel: +1-858-822-4771
>> Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
>> Web: www.awgoetz.de<http://www.awgoetz.de>
>>
>> On Apr 30, 2018, at 1:16 AM, Abhilash J <md.scfbio.gmail.com<mailto:md
>> .scfbio.gmail.com>> wrote:
>>
>> Hi everyone,
>>
>> I am trying to perform QM/MM MD on a ligand and some residues in the
>> active site of a protein.
>> I did a 10 ns production of the complex using classical MD then tried
>> minimization using QM/MM in AMBER with Gaussian.
>> I am getting linear minimization error on one of the water molecules
>> in the bulk water around the protein.
>> I tried different initial structures but the problem persists. (Every
>> time error was with a water residue in the bulk, only the residue number
>> changed)
>> I do not understand how the structure is running ok with GPU but not
>> getting into LINMIN error in CPU(s).
>> I also removed all but 1 water molecule from the list of atoms for QM
>> problem still persisted.
>> I tried changing number of CPUs in both gaussian and sander (sander
>> and sander.MPI).
>> I am using AMBER 18 with Gaussian 09
>>
>> *My input file is like this:*
>> ==========================================
>> Initial min of our structure QMMM
>> &cntrl
>> imin=1, maxcyc=2000, ncyc=1000,
>> cut=8.0, ntb=1, ntc=2, ntf=2,
>> ifqnt=1
>> /
>> &qmmm
>> qmmask=':429'
>> qmcharge=0,
>> qmshake=0,
>> qm_ewald=0, qm_pme=1,
>> qm_theory='EXTERN',
>> spin=1,
>> /
>> &gau
>> mem = '25GB',
>> method = 'B3LYP',
>> basis = '6-31G(d)',
>> num_threads = 12,
>> use_template = 0,
>> /
>> ==========================================
>>
>>
>> *Error on CPU using sander is like this:*
>> ===========================================
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 950 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
>>
>> BOND = 296.7775 ANGLE = 1192.8399 DIHED =
>> 4758.5891
>> VDWAALS = 8241.4047 EEL = -162581.2527 HBOND =
>> 0.0000
>> 1-4 VDW = 1340.3387 1-4 EEL = 18890.8303 RESTRAINT =
>> 0.0000
>> EXTERNESCF = -47974.7606
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1000 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
>>
>> BOND = 296.7775 ANGLE = 1192.8392 DIHED =
>> 4758.5888
>> VDWAALS = 8241.4014 EEL = -162581.2432 HBOND =
>> 0.0000
>> 1-4 VDW = 1340.3386 1-4 EEL = 18890.8303 RESTRAINT =
>> 0.0000
>> EXTERNESCF = -47974.7606
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1050 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
>>
>> BOND = 296.7774 ANGLE = 1192.8391 DIHED =
>> 4758.5888
>> VDWAALS = 8241.4006 EEL = -162581.2406 HBOND =
>> 0.0000
>> 1-4 VDW = 1340.3386 1-4 EEL = 18890.8303 RESTRAINT =
>> 0.0000
>> EXTERNESCF = -47974.7606
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1100 -1.7584E+05 1.4842E+01 5.0996E+01 O 14380
>>
>> BOND = 296.7774 ANGLE = 1192.8388 DIHED =
>> 4758.5887
>> VDWAALS = 8241.3995 EEL = -162581.2369 HBOND =
>> 0.0000
>> 1-4 VDW = 1340.3385 1-4 EEL = 18890.8302 RESTRAINT =
>> 0.0000
>> EXTERNESCF = -47974.7606
>>
>> ... RESTARTED DUE TO LINMIN FAILURE ...
>>
>> ***** REPEATED LINMIN FAILURE *****
>>
>> ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO
>> *****
>>
>>
>> ===========================================
>>
>>
>> *pmemd.cuda output is like this:*
>> ===========================================
>> NSTEP = 3350000 TIME(PS) = 12100.000 TEMP(K) = 298.79 PRESS =
>> 348.3
>> Etot = -95866.3616 EKtot = 24492.4648 EPtot =
>> -120358.8265
>> BOND = 1220.3755 ANGLE = 3352.1816 DIHED =
>> 5147.2619
>> 1-4 NB = 1494.6215 1-4 EEL = 18923.0385 VDWAALS =
>> 11982.1028
>> EELEC = -162485.2678 EHBOND = 0.0000 RESTRAINT =
>> 6.8594
>> EAMBER (non-restraint) = -120365.6859
>> EKCMT = 9700.3856 VIRIAL = 6770.2280 VOLUME =
>> 389629.2225
>> Density =
>> 1.0463
>> ------------------------------------------------------------
>> ------------------
>>
>> NMR restraints: Bond = 6.859 Angle = 0.000 Torsion = 0.000
>> ============================================================
>> ===================
>> ===========================================
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Received on Tue May 01 2018 - 09:00:03 PDT
