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.
*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 *WARNING 2* [file em.mdp]: The sum of the two largest charge group radii (7.005889) is larger than rlist (1.000000 *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]> 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]>> >> >> >> 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]>> 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]> >> >> 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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