yes its POPC at the top and SOL at the bottom. But the atoms names are not same that is the problem. ...
I am pasting the part of the gro file from where the problem has started. At 129 position the atom name is OW1 where as in topol file it is OW. Please guide me what should be done. 128POP C50 6654 4.864 -0.191 3.551 128POP CA1 6655 5.688 0.221 3.577 128POP CA2 6656 5.641 0.199 3.433 129SOL OW1 6657 5.223 1.492 0.817 129SOL HW2 6658 5.129 1.491 0.783 129SOL HW3 6659 5.277 1.423 0.769 130SOL OW1 6660 3.403 3.481 1.092 130SOL HW2 6661 3.313 3.523 1.107 130SOL HW3 6662 3.391 3.383 1.076 131SOL OW1 6663 3.852 2.274 0.985 131SOL HW2 6664 3.949 2.292 0.969 131SOL HW3 6665 3.811 2.353 1.030 132SOL OW1 6666 2.283 4.574 6.734 132SOL HW2 6667 2.231 4.637 6.675 132SOL HW3 6668 2.364 4.543 6.685 133SOL OW1 6669 2.569 2.428 5.841 133SOL HW2 6670 2.623 2.469 5.914 133SOL HW3 6671 2.629 2.372 5.783 134SOL OW1 6672 4.126 0.240 5.606 134SOL HW2 6673 4.180 0.312 5.562 134SOL HW3 6674 4.182 0.159 5.620 135SOL OW1 6675 5.968 3.911 5.734 135SOL HW2 6676 5.903 3.964 5.679 135SOL HW3 6677 6.042 3.878 5.675 136SOL OW1 6678 5.884 2.082 0.044 136SOL HW2 6679 5.824 2.156 0.076 136SOL HW3 6680 5.860 2.060 -0.051 137SOL OW1 6681 3.169 2.752 1.170 137SOL HW2 6682 3.250 2.714 1.214 137SOL HW3 6683 3.169 2.727 1.073 138SOL OW1 6684 5.521 5.906 6.408 138SOL HW2 6685 5.601 5.848 6.422 138SOL HW3 6686 5.480 5.927 6.497 139SOL OW1 6687 5.333 3.675 1.289 139SOL HW2 6688 5.387 3.677 1.205 139SOL HW3 6689 5.338 3.584 1.330 140SOL OW1 6690 3.167 5.794 0.240 140SOL HW2 6691 3.077 5.820 0.204 140SOL HW3 6692 3.237 5.854 0.203 Thanks in advance... Swati On Thu, Mar 21, 2013 at 11:18 AM, Emanuel Birru <emanuel.bi...@monash.edu>wrote: > If the atom names in your gro file and in the top file are the same then I > suggest to check how the sequence of the atoms looks like in your gro file. > Is it POPC at the top and the water at the bottom as your topology > suggested? If not swap them in the molecule section. > > [ molecules ] > ; molecule name nr. > POPC 128 ??? > SOL 2460 ??? > > Cheers, > EB > > > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of swati rana > Sent: Thursday, 21 March 2013 4:37 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] number of coordinates in coordinate file > (system.gro, 10019) does not match topology (topol.top, 17093) > > Dear Justin, > > I am facing another problem i.e. IN removing the periodicity of the > downloaded popc128a.pdb file. > > Warning: atom name 6673 in topol_popc.top and popc128a.gro does not match > (HW1 - HW2) > Warning: atom name 6674 in topol_popc.top and popc128a.gro does not match > (HW2 - HW3) > Warning: atom name 6675 in topol_popc.top and popc128a.gro does not match > (OW - OW1) > Warning: atom name 6676 in topol_popc.top and popc128a.gro does not match > (HW1 - HW2) > (more than 20 non-matching atom names) > > WARNING 1 [file topol_popc.top, line 31]: > 7380 non-matching atom names > atom names from topol_popc.top will be used > atom names from popc128a.gro will be ignored > > This question has been asked by another person as well and in case the > solution he suggested worked. But in my case everything in the pdb file is > okie though i am getting this error. Please suggest what should be done. > > spc.itp file is like this: > > [ moleculetype ] > ; molname nrexcl > SOL 2 > > [ atoms ] > ; nr type resnr residue atom cgnr charge mass > #ifndef HEAVY_H > 1 OW 1 SOL OW 1 -0.82 15.99940 > 2 H 1 SOL HW1 1 0.41 1.00800 > 3 H 1 SOL HW2 1 0.41 1.00800 > #else > 1 OW 1 SOL OW 1 -0.82 9.95140 > 2 H 1 SOL HW1 1 0.41 4.03200 > 3 H 1 SOL HW2 1 0.41 4.03200 > #endif > > #ifndef FLEXIBLE > [ settles ] > ; OW funct doh dhh > 1 1 0.1 0.16330 > > [ exclusions ] > 1 2 3 > 2 1 3 > 3 1 2 > #else > [ bonds ] > ; i j funct length force.c. > 1 2 1 0.1 345000 0.1 345000 > 1 3 1 0.1 345000 0.1 345000 > > [ angles ] > ; i j k funct angle force.c. > 2 1 3 1 109.47 383 109.47 383 > #endif > > And topol file is: > > ; > ; File 'topol_popc.top' was generated > ; By user: swati (1000) > ; On host: laptop > ; At date: Wed Feb 27 14:16:52 2013 > ; > ; This is your topology file > ; > ; Include chain topologies > #include "gromos43a1_lipid.ff/forcefield.itp" > > ; Include ligand toplogy > #include "gromos43a1_lipid.ff/ligand.itp" > > ; Include lipid topology > #include "popc.itp" > > ; Include water topology > #include "gromos43a1_lipid.ff/spc.itp" > > ; Include ion topologies > #include "gromos43a1_lipid.ff/ions.itp" > > ; System specifications > [ system ] > 128-Lipid POPC Bilayer > > [ molecules ] > ; molecule name nr. > POPC 128 > SOL 2460 > > Thanks in advance. > > With Regards, > Swati. > > > > On Mon, Mar 4, 2013 at 12:45 PM, swati rana <swati.rana...@gmail.com> > wrote: > > > Dear Justin, > > > > Thanks a lot, your suggestions helped me a lot. > > > > With Regards, > > Swati > > > > > > On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > >> > >> > >> On 3/2/13 1:42 AM, swati rana wrote: > >> > >>> Hi Justin, > >>> > >>> Thanks a lot, that suggestion of yours helped. I am on the > >>> equilibration step and its running but nothing is happening on the > >>> terminal its just stagnant. Is it fine because its more than 17 hrs > >>> now. Is there some problem. > >>> After running the second command nothing is happening on the terminal. > >>> > >>> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr > >>> > >>> mdrun -deffnm nvt > >>> > >>> I am sorry as it is not a reasonable question to ask but i am just > >>> asking out of curiosity and lack of time. > >>> > >>> > >> If you're trying to run an MD simulation in serial, you'll get > >> terrible performance unless the system is very small (a few hundred > >> atoms). Most MD is conducted in parallel on high-performance > >> computing clusters, or at the very least on a multi-core workstation, > again using parallelization. > >> > >> You won't get constant output in either case, since I/O is buffered > >> and write intervals depend on what you specify in the .mdp file. In > >> any case, if you're getting poor performance, you're probably simply > >> asking your computer to do something it's incapable of handling > efficiently. > >> > >> > >> -Justin > >> > >> -- > >> ==============================**========== > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gr > >> omacs.org/mailman/listinfo/gmx-users> > >> * Please search the archive at http://www.gromacs.org/** > >> Support/Mailing_Lists/Search< > 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<http://www.gromacs.org > >> /Support/Mailing_Lists> > >> > > > > > -- > 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 > -- > 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? 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