Quoting shikha agarwal <shikhaiiit...@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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists