Dr. Anselm Horn
Thank you ver much. And I am trying to solve it.
Xinxin Zhu
> -----原始邮件-----
> 发件人: "Dr. Anselm Horn" <anselm.horn.fau.de>
> 发送时间: 2022-05-27 18:11:24 (星期五)
> 收件人: amber.ambermd.org
> 抄送:
> 主题: Re: [AMBER] The failure on energy minimization
>
> Xinxin,
>
> the output file contains a distinct error message about an input issue.
> Maybe you want to adress that.
>
> Regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> On 05/27/2022 10:55 AM, 朱鑫鑫 wrote:
> > Dear experts
> >
> >
> >
> >
> > I don't know why the energy minimization will not success, when I input the following command lines: sander -O -i min.in -o min.out -p N559_sov.prmtop -c N559_sov.inpcrd -r min.rst -inf min.mdinfo.
> >
> >
> > -------------------------------------------------------
> > Amber 21 SANDER 2021
> > -------------------------------------------------------
> >
> > | Run on 05/27/2022 at 16:40:47
> >
> > | Executable path: sander
> > | Working directory: /opt/data/zhuxinxin/N559
> > | Hostname: Unknown
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: min.in
> > | MDOUT: min.out
> > |INPCRD: N559_sov.inpcrd
> > | PARM: N559_sov.prmtop
> > |RESTRT: min.rst
> > | REFC: refc
> > | MDVEL: mdvel
> > | MDFRC: mdfrc
> > | MDEN: mden
> > | MDCRD: mdcrd
> > |MDINFO: min.mdinfo
> > | MTMD: mtmd
> > |INPDIP: inpdip
> > |RSTDIP: rstdip
> > |INPTRA: inptraj
> >
> >
> > Here is the input file:
> >
> > Minimization with Cartesian restraints for the solute
> > &cntrl
> > imin=1,ntb=0,maxcyc=200,
> > ntpr=5,
> > cut=1000.,
> > igb=8,
> > ntr=1,
> > /
> >
> > --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> > --------------------------------------------------------------------------------
> >
> > | Flags:
> > | New format PARM file being parsed.
> > | Version = 1.000 Date = 05/27/22 Time = 13:34:02
> > NATOM = 116380 NTYPES = 18 NBONH = 85137 MBONA = 31295
> > NTHETH = 9368 MTHETA = 5872 NPHIH = 18828 MPHIA = 18640
> > NHPARM = 0 NPARM = 0 NNB = 234933 NRES = 27623
> > NBONA = 31295 NTHETA = 5872 NPHIA = 18640 NUMBND = 73
> > NUMANG = 166 NPTRA = 192 NATYP = 38 NPHB = 0
> > IFBOX = 2 NMXRS = 24 IFCAP = 0 NEXTRA = 27005
> > NCOPY = 0
> >
> > Implicit solvent radii are modified Bondi radii (mbondi)
> > Replacing prmtop screening parameters with GBn2 (igb=8) values
> > | CMAP information read from topology file:
> >
> > | Memory Use Allocated
> > | Real 11110874
> > | Hollerith 376765
> > | Integer 2539701
> > | Max Pairs 1
> > | nblistReal 0
> > | nblist Int 0
> > | Total 98196 kbytes
> >
> > | Note: 1-4 EEL scale factors are being read from the topology file.
> >
> > | Note: 1-4 VDW scale factors are being read from the topology file.
> > | Duplicated 0 dihedrals
> > | Duplicated 0 dihedrals
> > |CMAP: Reticulating splines.
> >
> > BOX TYPE: TRUNCATED OCTAHEDRON
> >
> > --------------------------------------------------------------------------------
> > 2. CONTROL DATA FOR THE RUN
> > --------------------------------------------------------------------------------
> >
> > default_name
> >
> > General flags:
> > imin = 1, nmropt = 0
> >
> > Nature and format of input:
> > ntx = 1, irest = 0, ntrx = 1
> >
> > Nature and format of output:
> > ntxo = 2, ntpr = 5, ntrx = 1, ntwr = 1
> > iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
> > ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0
> >
> > Potential function:
> > ntf = 1, ntb = 0, igb = 8, nsnb = 25
> > ipol = 0, gbsa = 0, iesp = 0
> > dielc = 1.00000, cut =1000.00000, intdiel = 1.00000
> > saltcon = 0.00000, offset = 0.19514, surften = 0.00500
> > rdt = 0.00000, rgbmax = 25.00000 extdiel = 78.50000
> > alpb = 0
> > gbalphaH = 0.78844, gbbetaH = 0.79870, gbgammaH = 0.43733
> > gbalphaC = 0.73376, gbbetaC = 0.50638, gbgammaC = 0.20584
> > gbalphaN = 0.50336, gbbetaN = 0.31683, gbgammaN = 0.19292
> > gbalphaOS = 0.86781, gbbetaOS = 0.87664, gbgammaOS = 0.38788
> > gbalphaP = 1.00000, gbbetaP = 0.80000, gbgammaP = 4.85000
> > gb_alpha_hnu = 0.53705, gb_beta_hnu = 0.36286, gb_gamma_hnu = 0.11670
> > gb_alpha_cnu = 0.33167, gb_beta_cnu = 0.19684, gb_gamma_cnu = 0.09342
> > gb_alpha_nnu = 0.68631, gb_beta_nnu = 0.46319, gb_gamma_nnu = 0.13872
> > gb_alpha_onu = 0.60634, gb_beta_onu = 0.46301, gb_gamma_onu = 0.14226
> > gb_alpha_pnu = 0.41836, gb_beta_pnu = 0.29005, gb_gamma_pnu = 0.10642
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 1
> > restraint_wt = 0.00000
> >
> > Energy minimization:
> > maxcyc = 200, ncyc = 10, ntmin = 1
> > dx0 = 0.01000, drms = 0.00010
> >
> > Extra-points options:
> > frameon = 0, chngmask= 0
> > Cannot use igb>0 (except igb=6) with extra-point force fields
> >
> > *** input error(s)
> >
> >
> >
> >
> >
> >
> >
> >
> > Please consult where is my incorrect operation, Thank you very much. And when I read turorials on amber website, I found several formats were used in sander, prmtop,inpcrd, and parm7, rst7, rst. So, I also want to where I can found the characterizations on these formats. I can't understan their differences. Thank you very much.
> >
> >
> >
> >
> > Xinxin Zhu
> >
> > 27/5/2022
> >
> >
> >
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> >
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> >
>
>
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Received on Fri May 27 2022 - 05:00:03 PDT
