AMBER Archive (2008)

Subject: Re: AMBER: Setting GROUP for pmemd

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 30 2008 - 18:28:37 CDT

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
>>>> To post, send mail to amber_at_scripps.edu
>>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>>> to majordomo_at_scripps.edu
>>>>
>>>
>>> -----------------------------------------------------------------------
>>> The AMBER Mail Reflector
>>> To post, send mail to amber_at_scripps.edu
>>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>>> to majordomo_at_scripps.edu
>>>
>> -----------------------------------------------------------------------
>> The AMBER Mail Reflector
>> To post, send mail to amber_at_scripps.edu
>> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>> to majordomo_at_scripps.edu
>>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>


  • application/octet-stream attachment: equil4.in

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu