[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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