AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 31 2008 - 01:25:44 CDT

It works. I did very badly. I had two examples of GROUP statements
that worked well in preliminary minimization - with either POPC
restrained or not - where END was in the first column ...

I apologize.
francesco

On Fri, Oct 31, 2008 at 3:02 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
> 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
>>>>>>
>>>>>> -----------------------------------------------------------------------
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>>>>>>
>>>>>
>>>>> -----------------------------------------------------------------------
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>>>>>
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>>>
>>> -----------------------------------------------------------------------
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>>
>
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