Dear Justin, I rearranged conf.gro but Gromacs is giving the same errors again. I think I am going mad :-( *conf.gro* 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 00:37 tarihinde Justin A. Lemkul <[email protected]> yazdı: > > > ahmet yıldırım wrote: > >> 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 >> > > Well, if my monospace font is any indication, yes, you have column > misalignment in the coordinates that could be causing a problem regarding > charge group size. I also don't know if the identical residue number will > cause a problem between your two PO4 molecules, but it might. > > The other issue about mismatched atom names is a combination of the > coordinate file and topology not agreeing with respect to their order. > > -Justin > > 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 <[email protected] <mailto: >> [email protected]>> 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 <[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> >> <mailto:[email protected]>>> 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 <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> >> <mailto:[email protected] <mailto:[email protected] >> >>>> >> >> >> >> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. >> Use the www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>. >> >> 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> <http://vt.edu> | (540) >> >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> 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 [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Ahmet YILDIRIM
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