[gmx-users] Re: methanol simulation error
Hi Mark, her is my topology, best wishes mustafa ; ;File 'topol.top' was generated ;By user: onbekend (0) ;On host: onbekend ;At date: Fri Jan 7 00:19:16 2011 ; ;This is a standalone topology file ; ;It was generated using program: ;pdb2gmx - VERSION 4.5.1 ; ;Command line was: ;pdb2gmx -f vpgvg10.pdb -ignh ; ;Force field was read from the standard Gromacs share directory. ; ; Include forcefield parameters #include gromos43a1.ff/forcefield.itp [ moleculetype ] ; Namenrexcl Protein 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeBchargeB massB ; residue 1 VAL rtp VAL q +1.0 1 NL 1VAL N 1 0.12914.0067 ; qtot 0.129 2 H 1VAL H1 1 0.248 1.008 ; qtot 0.377 3 H 1VAL H2 1 0.248 1.008 ; qtot 0.625 4 H 1VAL H3 1 0.248 1.008 ; qtot 0.873 5CH1 1VAL CA 2 0.127 13.019 ; qtot 1 6CH1 1VAL CB 2 0 13.019 ; qtot 1 7CH3 1VALCG1 2 0 15.035 ; qtot 1 8CH3 1VALCG2 2 0 15.035 ; qtot 1 9 C 1VAL C 3 0.38 12.011 ; qtot 1.38 10 O 1VAL O 3 -0.3815.9994 ; qtot 1 ; residue 2 PRO rtp PRO q 0.0 11 N 2PRO N 4 014.0067 ; qtot 1 12CH1 2PRO CA 5 0 13.019 ; qtot 1 13CH2 2PRO CB 5 0 14.027 ; qtot 1 14CH2 2PRO CG 6 0 14.027 ; qtot 1 15CH2 2PRO CD 6 0 14.027 ; qtot 1 16 C 2PRO C 7 0.38 12.011 ; qtot 1.38 17 O 2PRO O 7 -0.3815.9994 ; qtot 1 ; residue 3 GLY rtp GLY q 0.0 18 N 3GLY N 8 -0.2814.0067 ; qtot 0.72 19 H 3GLY H 8 0.28 1.008 ; qtot 1 20CH2 3GLY CA 9 0 14.027 ; qtot 1 21 C 3GLY C 10 0.38 12.011 ; qtot 1.38 22 O 3GLY O 10 -0.3815.9994 ; qtot 1 ; residue 4 VAL rtp VAL q 0.0 23 N 4VAL N 11 -0.2814.0067 ; qtot 0.72 24 H 4VAL H 11 0.28 1.008 ; qtot 1 25CH1 4VAL CA 12 0 13.019 ; qtot 1 26CH1 4VAL CB 12 0 13.019 ; qtot 1 27CH3 4VALCG1 12 0 15.035 ; qtot 1 28CH3 4VALCG2 12 0 15.035 ; qtot 1 29 C 4VAL C 13 0.38 12.011 ; qtot 1.38 30 O 4VAL O 13 -0.3815.9994 ; qtot 1 ; residue 5 GLY rtp GLY q 0.0 31 N 5GLY N 14 -0.2814.0067 ; qtot 0.72 32 H 5GLY H 14 0.28 1.008 ; qtot 1 33CH2 5GLY CA 15 0 14.027 ; qtot 1 34 C 5GLY C 16 0.38 12.011 ; qtot 1.38 35 O 5GLY O 16 -0.3815.9994 ; qtot 1 ; residue 6 VAL rtp VAL q 0.0 36 N 6VAL N 17 -0.2814.0067 ; qtot 0.72 37 H 6VAL H 17 0.28 1.008 ; qtot 1 38CH1 6VAL CA 18 0 13.019 ; qtot 1 39CH1 6VAL CB 18 0 13.019 ; qtot 1 40CH3 6VALCG1 18 0 15.035 ; qtot 1 41CH3 6VALCG2 18 0 15.035 ; qtot 1 42 C 6VAL C 19 0.38 12.011 ; qtot 1.38 43 O 6VAL O 19 -0.3815.9994 ; qtot 1 ; residue 7 PRO rtp PRO q 0.0 44 N 7PRO N 20 014.0067 ; qtot 1 45CH1 7PRO CA 21 0 13.019 ; qtot 1 46CH2 7PRO CB 21 0 14.027 ; qtot 1 47CH2 7PRO CG 22 0 14.027 ; qtot 1 48CH2 7PRO CD 22 0 14.027 ; qtot 1 49 C 7PRO C 23 0.38 12.011 ; qtot 1.38 50 O 7PRO O 23 -0.3815.9994 ; qtot 1 ; residue 8 GLY rtp GLY q 0.0 51 N 8GLY N 24 -0.28
Re: [gmx-users] Re: methanol simulation error
mustafa bilsel wrote: snip ; Include Position restraint file #ifdef POSRES #include posre.itp #endif ; Include water topology #include gromos43a1.ff/methanol.itp This topology defines the [moleculetype] name as Methanol, which is the name that needs to be used in the [molecules] directive below. But then, too, you're not using the same residue name either (MTH instead of MeOH), so it is still not possible to say what's going wrong. -Justin [ system ] ; Name Protein in methanol [ molecules ] ; Compound#mols Protein 1 MTH 660 -- 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 listgmx-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
