AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Robert Duke (rduke_at_email.unc.edu)
Date: Thu Oct 30 2008 - 21:02:05 CDT

Okay, the problem is primarily that you don't start the 'END' in column 1,
based on a very quick read of this very old code (this stuff was written
back in the 1980's, not by me - it works but is old fortran). You also have
3 blank lines at the end of the file; I don't think that is causing
problems, but I wouldn't take liberties with this stuff (and I don't want to
figure out everything that won't work...). So please try the modified file
I attached, with keywords starting in col 1 and the blank lines at the end
of the file removed.
Regards - Bob

----- Original Message -----
From: "Francesco Pietra" <chiendarret_at_gmail.com>
To: <amber_at_scripps.edu>
Sent: Thursday, October 30, 2008 7:28 PM
Subject: Re: AMBER: Setting GROUP for pmemd

> On Thu, Oct 30, 2008 at 11:30 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
>> Okay, the rfree() code involved here is directly taken from sander; very
>> minor mods. This stuff works all the time. What it looks like to me is
>> that the last END is getting misinterpreted as the start of another
>> group.
>> Can you please check it for nonprinting characters - try using 'od -c
>> mdin'. Make sure that there are no \r that you might have picked up from
>> a
>> windows system, or other nonprinting chars on the END card. There should
>> only be one \n at the end of the end - no trailing lines (not sure that
>> would actually be a problem, but this rgroup stuff is ancient. You
>> should
>> be able to confirm it is your input by running the same mdin in sander,
>> but
>> with nstlim = 1. If it runs in sander, but not pmemd, then I truly do
>> have
>> a problem. You still have not sent me the mdin like I requested,
>> either...
>> This has to be something crook about the mdin; this basic type of input
>> works all the time...
>> Regards - Bob
>
> You should not worry. There are no \r but sander.MPI gave the same
> error. Attached are the in and out files. Is that you wnated to have?
> Sorry if again I have not satisfied your request.
> Thanks
> francesco
>
>
>> ----- Original Message ----- From: "Francesco Pietra"
>> <chiendarret_at_gmail.com>
>> To: <amber_at_scripps.edu>
>> Sent: Thursday, October 30, 2008 5:56 PM
>> Subject: Re: AMBER: Setting GROUP for pmemd
>>
>>
>>> On Thu, Oct 30, 2008 at 8:29 PM, Robert Duke <rduke_at_email.unc.edu>
>>> wrote:
>>>>
>>>> Send the actual mdin files, along with a description of which did and
>>>> did
>>>> not work with pmemd vs. sander.MPI. I noted a caps error below in
>>>> something
>>>> that supposedly worked ("EnD" keyword). Just glancing at the code, I
>>>> do
>>>> believe the keywords are going to be case-sensitive.
>>>> Regards - Bob Duke
>>>
>>>
>>> The lower case "n" was a typo here only.
>>>
>>> With pmemd (all residues restrained except WAT) worked well:
>>>
>>> Steepest descent minimization to
>>> relax water only
>>> &cntrl
>>> imin=1, maxcyc=10000, ntmin=2,
>>> cut=10, ntb=1, ntpr=1, ntr=1
>>> /
>>> Keep protein, ligand and POPC fixed
>>> 32.0
>>> RES 1 341
>>> END
>>> END
>>>
>>>
>>> Steepest descent minimization to
>>> relax water and POPC
>>> &cntrl
>>> imin=1, maxcyc=10000, ntmin=2,
>>> cut=10, ntb=1, ntpr=1, ntr=1
>>> /
>>> Keep protein and ligand fixed
>>> 32.0
>>> RES 79 341
>>> END
>>> END
>>> ======================================================
>>>
>>> To restrain the polar heads only of POPC during heating (50ps) and
>>> equilibration (600ps in steps) (78 molecules of POPC are present in
>>> the box), I was unable formulate a valid mdin for pmemd. sander.MPI
>>> worked well with:
>>>
>>> Heating gradually complex_box with SHAKE and restraints on
>>> complex and polar heads of POPC
>>> &cntrl
>>> imin=0,irest=0, ntx=1,
>>> nstlim=25000, dt=0.002,
>>> cut=10,ntb=1,
>>> ntc=2,ntf=2,
>>> ntpr=500, ntwx=500,
>>> ntt=3, gamma_ln=2.0,
>>> tempi=0.0, temp0=300.0,
>>> ntr=1,
>>> restraintmask=":79-341 | :POP_at_O2, P1, O3, O4, O1, C15, C11, N, C12,
>>> C13,
>>> C14"
>>> restraint_wt=32,
>>> nmropt=1
>>> /
>>> &wt TYPE='TEMP0', istep1=0, istep2=25000,
>>> value1=0.1, value2=300.0, /
>>> &wt TYPE='END' /
>>>
>>>
>>> Equilibration, restraining protein, ligand, and polar heads of POPC
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> nstlim=25000, dt=0.002,
>>> cut=10, ntb=2, ntp=1, taup=2.0,
>>> ntc=2, ntf=2,
>>> ntpr=1000, ntwx=1000,
>>> ntt=3, gamma_ln=2.0,
>>> temp0=300.0,
>>> ntr=1,
>>> restraintmask=":79-341 | :POP_at_O2, P1, O3, O4, O1, C15, C11, N, C12,
>>> C13,
>>> C14"
>>> restraint_wt=32,
>>> /
>>> =================================
>>>
>>> To continue equilibration while restraining the protein and its ligand
>>> only (using the rst file from the last above equilibration), pmemd
>>> failed with:
>>>
>>> Equilibration, restraining protein and ligand
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> nstlim=25000, dt=0.002,
>>> cut=10, ntb=2, ntp=1, taup=2.0,
>>> ntc=2, ntf=2,
>>> ntpr=1000, ntwx=1000,
>>> ntt=3, gamma_ln=2.0,
>>> temp0=300.0,
>>> ntr=1,
>>> /
>>> Keep protein and ligand restrained
>>> 32.0
>>> RES 79 341
>>> END
>>> END
>>>
>>>
>>>
>>> The full out file reads:
>>>
>>> -------------------------------------------------------
>>> Amber 10 SANDER 2008
>>> -------------------------------------------------------
>>>
>>> | PMEMD implementation of SANDER, Release 10
>>>
>>> | Run on 10/30/2008 at 19:20:59
>>>
>>> [-O]verwriting output
>>>
>>> File Assignments:
>>> | MDIN: equil4.in
>>> | MDOUT: equil4.out
>>> | INPCRD: equil3.rst
>>> | PARM: complex_AA1_POP_BOX.prmtop
>>> | RESTRT: equil4.rst
>>> | REFC: equil3.rst
>>> | MDVEL: mdvel
>>> | MDEN: mden
>>> | MDCRD: equil4.mdcrd
>>> | MDINFO: mdinfo
>>> |LOGFILE: logfile
>>>
>>>
>>> Here is the input file:
>>>
>>> Equilibration, restraining protein and ligand
>>> &cntrl
>>> imin=0, irest=1, ntx=5,
>>> nstlim=25000, dt=0.002,
>>> cut=10, ntb=2, ntp=1, taup=2.0,
>>> ntc=2, ntf=2,
>>> ntpr=1000, ntwx=1000,
>>> ntt=3, gamma_ln=2.0,
>>> temp0=300.0,
>>> ntr=1,
>>>
>>> /
>>> Keep protein and ligand restrained
>>> 32.0
>>> RES 79 341
>>> END
>>> END
>>>
>>>
>>>
>>>
>>>
>>>
>>> | Conditional Compilation Defines Used:
>>> | DIRFRC_COMTRANS
>>> | DIRFRC_EFS
>>> | DIRFRC_NOVEC
>>> | MPI
>>> | SLOW_NONBLOCKING_MPI
>>> | PUBFFT
>>> | FFTLOADBAL_2PROC
>>> | MKL
>>>
>>> | Largest sphere to fit in unit cell has radius = 38.953
>>>
>>> | New format PARM file being parsed.
>>> | Version = 1.000 Date = 10/25/08 Time = 00:28:55
>>> | Duplicated 0 dihedrals
>>>
>>> | Duplicated 0 dihedrals
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> 1. RESOURCE USE:
>>>
>>> --------------------------------------------------------------------------------
>>>
>>> getting new box info from bottom of inpcrd
>>>
>>> NATOM = 84578 NTYPES = 19 NBONH = 78494 MBONA = 6046
>>> NTHETH = 20048 MTHETA = 7395 NPHIH = 33035 MPHIA = 15321
>>> NHPARM = 0 NPARM = 0 NNB = 174234 NRES = 23681
>>> NBONA = 6046 NTHETA = 7395 NPHIA = 15321 NUMBND = 65
>>> NUMANG = 130 NPTRA = 61 NATYP = 46 NPHB = 1
>>> IFBOX = 1 NMXRS = 134 IFCAP = 0 NEXTRA = 0
>>> NCOPY = 0
>>>
>>> | Coordinate Index Table dimensions: 18 16 12
>>> | Direct force subcell size = 6.0744 6.3260 6.4921
>>>
>>> BOX TYPE: RECTILINEAR
>>>
>>>
>>> --------------------------------------------------------------------------------
>>> 2. CONTROL DATA FOR THE RUN
>>>
>>> --------------------------------------------------------------------------------
>>>
>>>
>>>
>>> General flags:
>>> imin = 0, nmropt = 0
>>>
>>> Nature and format of input:
>>> ntx = 5, irest = 1, ntrx = 1
>>>
>>> Nature and format of output:
>>> ntxo = 1, ntpr = 1000, ntrx = 1, ntwr =
>>> 500
>>> iwrap = 0, ntwx = 1000, ntwv = 0, ntwe = 0
>>> ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
>>>
>>> Potential function:
>>> ntf = 2, ntb = 2, igb = 0, nsnb = 25
>>> ipol = 0, gbsa = 0, iesp = 0
>>> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>>> scnb = 2.00000, scee = 1.20000
>>>
>>> Frozen or restrained atoms:
>>> ibelly = 0, ntr = 1
>>>
>>> Molecular dynamics:
>>> nstlim = 25000, nscm = 1000, nrespa = 1
>>> t = 0.00000, dt = 0.00200, vlimit = 20.00000
>>>
>>> Langevin dynamics temperature regulation:
>>> ig = 71277
>>> temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
>>>
>>> Pressure regulation:
>>> ntp = 1
>>> pres0 = 1.00000, comp = 44.60000, taup = 2.00000
>>>
>>> SHAKE:
>>> ntc = 2, jfastw = 0
>>> tol = 0.00001
>>>
>>> | Intermolecular bonds treatment:
>>> | no_intermolecular_bonds = 1
>>>
>>> | Energy averages sample interval:
>>> | ene_avg_sampling = 1000
>>>
>>> Ewald parameters:
>>> verbose = 0, ew_type = 0, nbflag = 1, use_pme = 1
>>> vdwmeth = 1, eedmeth = 1, netfrc = 1
>>> Box X = 109.339 Box Y = 101.215 Box Z = 77.906
>>> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>>> NFFT1 = 120 NFFT2 = 108 NFFT3 = 80
>>> Cutoff= 10.000 Tol =0.100E-04
>>> Ewald Coefficient = 0.27511
>>> Interpolation order = 4
>>>
>>> | PMEMD ewald parallel performance parameters:
>>> | block_fft = 0
>>> | fft_blk_y_divisor = 2
>>> | excl_recip = 0
>>> | excl_master = 0
>>> | atm_redist_freq = 320
>>>
>>> LOADING THE CONSTRAINED ATOMS AS GROUPS
>>>
>>>
>>> 5. REFERENCE ATOM COORDINATES
>>>
>>>
>>> ----- READING GROUP 1; TITLE:
>>> Keep protein and ligand restrained
>>>
>>> GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
>>> GRP 1 RES 79 TO 341
>>> Number of atoms in this group = 4106
>>> ----- READING GROUP 2; TITLE:
>>> END
>>>
>>> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
>>>
>>> rfree: End of file on unit 5
>>> ============================
>>>
>>>
>>> francesco
>>>
>>>> ----- Original Message ----- From: "Francesco Pietra"
>>>> <chiendarret_at_gmail.com>
>>>> To: "Amber" <amber_at_scripps.edu>
>>>> Sent: Thursday, October 30, 2008 3:10 PM
>>>> Subject: AMBER: Setting GROUP for pmemd
>>>>
>>>>
>>>>> The pdb is
>>>>> RES 1 78 lipid POPC
>>>>>
>>>>> RES 79 340 protein with capping groups (included in numbering)
>>>>>
>>>>> RES 341 ligand
>>>>> ====
>>>>>
>>>>> Input for pmemd to restrain protein ligand and POPC (the other
>>>>> residues
>>>>> are WAT)
>>>>>
>>>>> /
>>>>> Keep ...
>>>>> 32.0
>>>>> RES 1 341
>>>>> END
>>>>> EnD
>>>>>
>>>>> worked fine.
>>>>> =========
>>>>>
>>>>> The I moved to sander.MPI in order to be able to restrain protein,
>>>>> ligand and a part only of lipid. Now back to pmemd to restrain protein
>>>>> and ligand only
>>>>>
>>>>>
>>>>> /
>>>>> Keep ..
>>>>> 32.0
>>>>> RES 79 341
>>>>> END
>>>>> END
>>>>>
>>>>> the out file:
>>>>> LOADING THE CONSTRAINED ATOMS AS GROUPS
>>>>> 5. REFERENCE ATOM AND COORDINATES
>>>>> READING GROUP 1;TITLE:
>>>>> GROUP 1 HAS HARMONIC CONSTRAINTS 32.00000
>>>>> GRP 1 RES 79 TO 341
>>>>> number of atoms ...
>>>>> READING GROUP 2; TITLE:
>>>>> END
>>>>> GROUP 2 HAS HARMONIC CONSTRAINTS 0.00000
>>>>> rfree: End of file on unit 5
>>>>> ====================
>>>>>
>>>>> Thanks a lot for pointing out my mistake.
>>>>>
>>>>> francesco pietra
>>>>> -----------------------------------------------------------------------
>>>>> The AMBER Mail Reflector
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>>>>> to majordomo_at_scripps.edu
>>>>>
>>>>
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>>
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>


  • application/octet-stream attachment: equil4.in

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