Dear Justin, But I doesn't see any error in the conf.gro. Am I wrong? *conf.gro:* LYSOZYME 2363 1MET N 1 0.556 -1.596 -0.893 ... 388HOH HW2 2353 1.763 -1.939 1.371 1PO4 O2 1 1.456 -2.557 1.128 1PO4 P 2 1.543 -2.651 1.204 1PO4 O3 3 1.507 -2.801 1.181 1PO4 O4 4 1.504 -2.632 1.354 1PO4 O1 5 1.690 -2.636 1.176 1PO4 O2 1 2.196 0.201 -1.915 1PO4 P 2 2.174 0.062 -1.865 1PO4 O3 3 2.062 -0.001 -1.948 1PO4 O4 4 2.142 0.066 -1.713 1PO4 O1 5 2.307 -0.006 -1.892 5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000 0.00000
19 Nisan 2011 00:12 tarihinde Justin A. Lemkul <jalem...@vt.edu> yazdı: > > > ahmet yıldırım wrote: > >> Dear Justin, >> >> Now, I added two PO4 to the coordinate file, then added two to the >> topology. I created PO4_1.gro and PO4_1.itp for first PO4 using PRODRG. >> Then, I created PO4_2.gro and PO4_2.itp for first PO4 using PRODRG. I added >> 10 atoms/lines into conf.gro from PO4.gro(5cordinate and PO4_2.gro files (5 >> coordinate), then 10 the second line of conf.gro. I used only one because of >> the same as PO4_1.itp and PO4_2.itp files. >> >> > That's exactly what you want to do - an .itp defines a [moleculetype]. If > you have two identical molecules that are defined by the same > [moleculetype], you don't want to #include the same thing twice. In fact, > grompp will throw a fatal error that your [moleculetype] is redefined. > Think of this analogy - you #include "spc.itp" in your system, but you > don't do it for every single water molecule individually. You define the > [moleculetype] and then define in the topology how many instances of that > particular molecule in the [molecules] directive. > > *_First PO4 from 3HTB:_* >> >> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 >> P HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 >> O HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 >> O HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 >> O HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 >> O >> *_second PO4 from 3HTB:_* >> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 >> P HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 >> O HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 >> O HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 >> O HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 >> O >> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro >> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro >> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr >> *WARNING 1* [file topol.top, line 10673]: >> 670 non-matching atom names >> atom names from topol.top will be used >> atom names from solvated.gro will be ignored >> > > As I said in my last message, the order of the contents of the coordinate > file and [molecules] directive must match. You have not satisfied this > requirement. > > *WARNING 2* [file em.mdp]: >> >> The sum of the two largest charge group radii (7.005889) is larger than >> rlist (1.000000 >> > > I have no idea what might cause this other than you've mangled the > coordinates in some way, or perhaps molecules are broken across periodic > boundaries. In a normal input file, the latter is not the case. My guess > is that your copying/pasting of coordinates is somehow at fault. > > -Justin > > *NOTE 1* [file topol.top, line 10673]: >> >> System has non-zero total charge: 2.000001e+00 >> *Fatal error:* >> Too many warnings (2), grompp terminated. >> If you are sure all warnings are harmless, use the -maxwarn option. >> >> >> >> >> 18 Nisan 2011 23:26 tarihinde Justin A. Lemkul <jalem...@vt.edu <mailto: >> jalem...@vt.edu>> yazdı: >> >> >> >> You said you added one PO4 to the coordinate file, but then added >> two to the topology. Hence the difference of exactly 5 atoms, or >> one PO4 molecule. >> >> The content of the coordinate file must always match the content of >> the topology, with respect to the number of atoms (based on the >> listing of molecules) and the order in which they appear in the >> [molecules] directive. >> >> -Justin >> >> >> >> 2011/4/18 lucioric <lucio...@ibt.unam.mx >> <mailto:lucio...@ibt.unam.mx> <mailto:lucio...@ibt.unam.mx >> >> <mailto:lucio...@ibt.unam.mx>>> >> >> >> You need to get or calculate parameters for phosphate. These >> parameters are yet calculated for the AMBER forcefield, there >> are in >> >> http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/cof/frcmod.phos >> . >> You need to install AmberTools and copy the frcmod.phos file >> in the >> URL above to the appropriate directory (see the AmberTools >> manual). >> Then, you can build the topology and coordinate files in AMBER >> format for your system using the tleap tool. These files in >> AMBER >> format can be converted to Gromacs format using the acpype >> program. >> With these files in Gromacs format you can run a MD in Gromacs, >> using the Amber forcefield. >> Lucio Montero >> Instituto de Biotecnologia, UNAM, Mexico. >> >> On Mon, 18 Apr 2011 20:40:49 +0300, ahmet yıldırım >> <ahmedo...@gmail.com <mailto:ahmedo...@gmail.com> >> <mailto:ahmedo...@gmail.com <mailto:ahmedo...@gmail.com>>> wrote: >> >> Dear Justin, >> >> You prepared a useful tutorial. if you used PO4 ligand >> (which has 2 >> molecule) instead of 1JZ4 ligand from 3HTB.pdb, Then, in the >> .itp and >> .gro files of ligand because of 2 molecule, what change? >> Can you give some hint? >> Thanks >> >> 3HTB.pdb >> .... >> >> TER 1365 ASN A 163 >> HETATM 1366 P PO4 A 165 15.430 -26.507 12.040 0.70 13.01 P >> HETATM 1367 O1 PO4 A 165 16.899 -26.359 11.761 0.70 8.42 O >> HETATM 1368 O2 PO4 A 165 14.565 -25.571 11.281 0.70 12.47 O >> >> HETATM 1369 O3 PO4 A 165 15.071 -28.010 11.811 0.70 11.58 O >> HETATM 1370 O4 PO4 A 165 15.042 -26.318 13.543 0.70 11.36 O >> HETATM 1371 P PO4 A 166 21.741 0.620 -18.648 0.50 20.49 P >> HETATM 1372 O1 PO4 A 166 23.073 -0.065 -18.917 0.50 18.04 O >> >> HETATM 1373 O2 PO4 A 166 21.958 2.010 -19.153 0.50 19.25 O >> HETATM 1374 O3 PO4 A 166 20.616 -0.014 -19.484 0.50 14.22 O >> HETATM 1375 O4 PO4 A 166 21.425 0.662 -17.127 0.50 15.77 O >> HETATM 1376 C4 JZ4 A 167 24.294 -24.124 -0.071 1.00 16.39 C >> >> .. >> >> >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- Ahmet YILDIRIM >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> -- >> Ahmet YILDIRIM >> > > -- > ======================================== > > 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 > -- Ahmet YILDIRIM
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