[gmx-users] Unknown bond_atomtype MNH3

Justin A. Lemkul jalemkul at vt.edu
Thu Dec 23 16:59:12 CET 2010


Quoting shikha agarwal <shikhaiiitabi at gmail.com>:

>  Hello Justin,
>
>     Thank you for your reply.
>
> I modifed ffG53a6bn_lipid.itp

This is not ffG53a6nb_lipid.itp, this is simply a modified lipid.itp to which it
looks like you've added a line for OW (which contains the wrong mass).  The
instructions in the tutorial direct you to copy the relevant information from
lipid.itp into ffG53a6nb.itp to create ffG53a6nb_lipid.itp.  So copy the
[atomtypes] from lipid.itp into the [atomtypes] from ffG53a6nb.itp, etc.

-Justin

> [ atomtypes ]
> ;name     mass     charge ptype  c6           c12
> ;
>    LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
>   LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
>   LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
>    LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
>   LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
>   LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
>    LP    30.9738    0.000  A 9.16000e-03 2.50700e-05 ;phosphor, OPLS
>   LOS    15.9994    0.000  A 2.56300e-03 1.86800e-06 ;ester oxygen, OPLS
>   LP2    14.0270    0.000  A 5.87400e-03 2.26500e-05 ;RB CH2, Bergers LJ
>   LP3    15.0350    0.000  A 8.77700e-03 3.38500e-05 ;RB CH3, Bergers LJ
>   LC3    15.0350    0.000  A 9.35700e-03 3.60900e-05 ;CH3, OPLS
>   LC2    14.0270    0.000  A 5.94700e-03 1.79000e-05 ;CH2, OPLS
>    OW    0.000      0.000  A 2.617345-03 2.63412e-06
> [ nonbond_params ]
> ; i    j    func    c6           c12
>    LO    LO     1 2.36400e-03  1.59000e-06
>    LO   LOM     1 2.36400e-03  1.59000e-06
>    LO   LNL     1 2.81600e-03  2.50600e-06
>    LO    LC     1 3.39900e-03  4.64800e-06
>    LO   LH1     1 3.08700e-03  4.39300e-06
>    LO   LH2     1 4.06900e-03  6.28300e-06
>    LO    LP     1 4.65300e-03  6.31300e-06
>    LO   LOS     1 2.46100e-03  1.72300e-06
>    LO   LP2     1 3.72700e-03  6.00000e-06
>    LO   LP3     1 4.55500e-03  7.33500e-06
>    LO   LC3     1 4.70300e-03  7.57400e-06
>    LO   LC2     1 3.74900e-03  5.33500e-06
>   LOM   LOM     1 2.36400e-03  1.59000e-06
>   LOM   LNL     1 2.81600e-03  2.50600e-06
>   LOM    LC     1 3.39900e-03  4.64800e-06
>   LOM   LH1     1 3.08700e-03  4.39300e-06
>   LOM   LH2     1 4.06900e-03  6.28300e-06
>   LOM    LP     1 4.65300e-03  6.31300e-06
>   LOM   LOS     1 2.46100e-03  1.72300e-06
>   LOM   LP2     1 3.72700e-03  6.00000e-06
>   LOM   LP3     1 4.55500e-03  7.33500e-06
>   LOM   LC3     1 4.70300e-03  7.57400e-06
>   LOM   LC2     1 3.74900e-03  5.33500e-06
>   LNL   LNL     1 3.35300e-03  3.95100e-06
>   LNL    LC     1 4.04900e-03  7.32800e-06
>   LNL   LH1     1 3.67700e-03  6.92500e-06
>   LNL   LH2     1 4.84600e-03  9.90500e-06
>   LNL    LP     1 5.54200e-03  9.95300e-06
>   LNL   LOS     1 2.93200e-03  2.71700e-06
>   LNL   LP2     1 4.43800e-03  9.46000e-06
>   LNL   LP3     1 5.42500e-03  1.15600e-05
>   LNL   LC3     1 5.60100e-03  1.19400e-05
>   LNL   LC2     1 4.46600e-03  8.41100e-06
>    LC    LC     1 4.88800e-03  1.35900e-05
>    LC   LH1     1 4.43900e-03  1.28400e-05
>    LC   LH2     1 5.85100e-03  1.83700e-05
>    LC    LP     1 6.69100e-03  1.84600e-05
>    LC   LOS     1 3.53900e-03  5.03800e-06
>    LC   LP2     1 5.35900e-03  1.75400e-05
>    LC   LP3     1 6.55000e-03  2.14500e-05
>    LC   LC3     1 6.76300e-03  2.21500e-05
>    LC   LC2     1 5.39100e-03  1.56000e-05
>   LH1   LH1     1 4.03100e-03  1.21400e-05
>   LH1   LH2     1 5.31300e-03  1.73600e-05
>   LH1    LP     1 6.07700e-03  1.74400e-05
>   LH1   LOS     1 3.21400e-03  4.76100e-06
>   LH1   LP2     1 4.86600e-03  1.65800e-05
>   LH1   LP3     1 5.94800e-03  2.02700e-05
>   LH1   LC3     1 6.14200e-03  2.09300e-05
>   LH1   LC2     1 4.89600e-03  1.47400e-05
>   LH2   LH2     1 7.00200e-03  2.48300e-05
>   LH2    LP     1 8.00900e-03  2.49500e-05
>   LH2   LOS     1 4.23600e-03  6.81000e-06
>   LH2   LP2     1 6.41400e-03  2.37100e-05
>   LH2   LP3     1 7.83900e-03  2.89900e-05
>   LH2   LC3     1 8.09500e-03  2.99300e-05
>   LH2   LC2     1 6.45300e-03  2.10800e-05
>    LP    LP     1 9.16000e-03  2.50700e-05
>    LP   LOS     1 4.84500e-03  6.84200e-06
>    LP   LP2     1 7.33500e-03  2.38300e-05
>    LP   LP3     1 8.96600e-03  2.91300e-05
>    LP   LC3     1 9.25800e-03  3.00800e-05
>    LP   LC2     1 7.38100e-03  2.11900e-05
>   LOS   LOS     1 2.56300e-03  1.86800e-06
>   LOS   LP2     1 3.88000e-03  6.50400e-06
>   LOS   LP3     1 4.74300e-03  7.95100e-06
>   LOS   LC3     1 4.89700e-03  8.21000e-06
>   LOS   LC2     1 3.90400e-03  5.78200e-06
>   LP2   LP2     1 5.87400e-03  2.26500e-05
>   LP2   LP3     1 7.18000e-03  2.76900e-05
>   LP2   LC3     1 7.41400e-03  2.85900e-05
>   LP2   LC2     1 5.91000e-03  2.01400e-05
>   LP3   LP3     1 8.77700e-03  3.38500e-05
>   LP3   LC3     1 9.06200e-03  3.49500e-05
>   LP3   LC2     1 7.22400e-03  2.46200e-05
>   LC3   LC3     1 9.35700e-03  3.60900e-05
>   LC3   LC2     1 7.45900e-03  2.54200e-05
>   LC2   LC2     1 5.94700e-03  1.79000e-05
> ;; lipid-SPC/SPCE interactions
>    LO    OW    1 2.50200e-03  2.06700e-06
>   LOM    OW    1 2.50200e-03  2.06700e-06
>   LNL    OW    1 2.98000e-03  3.25900e-06
>    LC    OW    1 3.59800e-03  6.04400e-06
>   LH1    OW    1 3.26800e-03  5.71200e-06
>   LH2    OW    1 4.30700e-03  8.17000e-06
>    LP    OW    1 4.92600e-03  8.21000e-06
>   LOS    OW    1 2.60500e-03  2.24100e-06
>   LP2    OW    1 3.94400e-03  7.80300e-06
>   LP3    OW    1 4.82100e-03  9.53900e-06
>   LC3    OW    1 4.97800e-03  9.85000e-06
>   LC2    OW    1 3.96900e-03  6.93800e-06
>
> [ pairtypes ]
> ; i    j    func   cs6          cs12
>    LO    LO     1 2.95200e-04  1.98700e-07
>    LO   LOM     1 2.95200e-04  1.98700e-07
>    LO    OW     1 3.12800e-04  2.58400e-07
>    LO   LNL     1 3.51800e-04  3.13300e-07
>    LO    LC     1 4.24600e-04  5.80900e-07
>    LO   LH1     1 3.85500e-04  5.49000e-07
>    LO   LH2     1 5.08200e-04  7.85200e-07
>    LO    LP     1 5.81300e-04  7.89000e-07
>    LO   LOS     1 3.07500e-04  2.15300e-07
>    LO   LP2     1 4.65700e-04  7.50000e-07
>    LO   LP3     1 5.69000e-04  9.16800e-07
>    LO   LC3     1 5.87600e-04  9.46600e-07
>    LO   LC2     1 4.68500e-04  6.66800e-07
>   LOM   LOM     1 2.95200e-04  1.98700e-07
>   LOM    OW     1 3.12800e-04  2.58400e-07
>   LOM   LNL     1 3.51800e-04  3.13300e-07
>   LOM    LC     1 4.24600e-04  5.80900e-07
>   LOM   LH1     1 3.85500e-04  5.49000e-07
>   LOM   LH2     1 5.08200e-04  7.85200e-07
>   LOM    LP     1 5.81300e-04  7.89000e-07
>   LOM   LOS     1 3.07500e-04  2.15300e-07
>   LOM   LP2     1 4.65700e-04  7.50000e-07
>   LOM   LP3     1 5.69000e-04  9.16800e-07
>   LOM   LC3     1 5.87600e-04  9.46600e-07
>   LOM   LC2     1 4.68500e-04  6.66800e-07
>    OW   LNL     1 3.72700e-04  4.07400e-07
>    OW    LC     1 4.49800e-04  7.55600e-07
>    OW   LH1     1 4.08500e-04  7.14100e-07
>    OW   LH2     1 5.38500e-04  1.02100e-06
>    OW    LP     1 6.15900e-04  1.02600e-06
>    OW   LOS     1 3.25800e-04  2.80100e-07
>    OW   LP2     1 4.93400e-04  9.75400e-07
>    OW   LP3     1 6.02900e-04  1.19200e-06
>    OW   LC3     1 6.22600e-04  1.23100e-06
>    OW   LC2     1 4.96400e-04  8.67300e-07
>   LNL   LNL     1 4.19200e-04  4.94000e-07
>   LNL    LC     1 5.05900e-04  9.16100e-07
>   LNL   LH1     1 4.59400e-04  8.65700e-07
>   LNL   LH2     1 6.05600e-04  1.23800e-06
>   LNL    LP     1 6.92700e-04  1.24400e-06
>   LNL   LOS     1 3.66500e-04  3.39600e-07
>   LNL   LP2     1 5.54900e-04  1.18300e-06
>   LNL   LP3     1 6.78100e-04  1.44600e-06
>   LNL   LC3     1 7.00300e-04  1.49300e-06
>   LNL   LC2     1 5.58300e-04  1.05100e-06
>    LC    LC     1 6.10600e-04  1.69900e-06
>    LC   LH1     1 5.54500e-04  1.60500e-06
>    LC   LH2     1 7.30800e-04  2.29600e-06
>    LC    LP     1 8.36000e-04  2.30700e-06
>    LC   LOS     1 4.42200e-04  6.29700e-07
>    LC   LP2     1 6.69700e-04  2.19300e-06
>    LC   LP3     1 8.18300e-04  2.68100e-06
>    LC   LC3     1 8.45100e-04  2.76800e-06
>    LC   LC2     1 6.73700e-04  1.95000e-06
>   LH1   LH1     1 5.03500e-04  1.51700e-06
>   LH1   LH2     1 6.63700e-04  2.17000e-06
>   LH1    LP     1 7.59200e-04  2.18000e-06
>   LH1   LOS     1 4.01600e-04  5.95100e-07
>   LH1   LP2     1 6.08200e-04  2.07300e-06
>   LH1   LP3     1 7.43100e-04  2.53400e-06
>   LH1   LC3     1 7.67400e-04  2.61600e-06
>   LH1   LC2     1 6.11800e-04  1.84300e-06
>   LH2   LH2     1 8.74800e-04  3.10400e-06
>   LH2    LP     1 1.00100e-03  3.11900e-06
>   LH2   LOS     1 5.29400e-04  8.51200e-07
>   LH2   LP2     1 8.01600e-04  2.96400e-06
>   LH2   LP3     1 9.79500e-04  3.62400e-06
>   LH2   LC3     1 1.01200e-03  3.74200e-06
>   LH2   LC2     1 8.06500e-04  2.63600e-06
>    LP    LP     1 1.14500e-03  3.13300e-06
>    LP   LOS     1 6.05500e-04  8.55200e-07
>    LP   LP2     1 9.16900e-04  2.97800e-06
>    LP   LP3     1 1.12000e-03  3.64100e-06
>    LP   LC3     1 1.15700e-03  3.76000e-06
>    LP   LC2     1 9.22500e-04  2.64800e-06
>   LOS   LOS     1 3.20300e-04  2.33400e-07
>   LOS   LP2     1 4.85100e-04  8.12900e-07
>   LOS   LP3     1 5.92700e-04  9.93800e-07
>   LOS   LC3     1 6.12100e-04  1.02600e-06
>   LOS   LC2     1 4.88000e-04  7.22800e-07
>   LP2   LP2     1 7.34600e-04  2.83100e-06
>   LP2   LP3     1 8.97500e-04  3.46100e-06
>   LP2   LC3     1 9.26900e-04  3.57400e-06
>   LP2   LC2     1 7.39000e-04  2.51700e-06
>   LP3   LP3     1 1.09700e-03  4.23100e-06
>   LP3   LC3     1 1.13300e-03  4.36900e-06
>   LP3   LC2     1 9.03000e-04  3.07700e-06
>   LC3   LC3     1 1.17000e-03  4.51100e-06
>   LC3   LC2     1 9.32500e-04  3.17700e-06
>   LC2   LC2     1 7.43500e-04  2.23800e-06
>
>
>
> now " Atomtype 'OW' not found!" is not occuring .But new error
> "Unknown bond_atomtype MNH3" occuring .
>
>  to create ffG53a6bon_lipid.itp  I only modified the last  lines of
> ffG53a6bn_lipid.itp as per tutorial
>
>
> [ dihedraltypes ]
> S      S      1   gd_21
> NR     FE     1   gd_38
> CH2    S      1   gd_26
> LP2 LP2  3   9.2789   12.156  -13.120 -3.0597 26.240 -31.495
> LH2 LH2  3   9.2789   12.156  -13.120 -3.0597 26.240 -31.495
>
>
> help me!
>
> regards:
> shikha
>


========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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