Hello everyone, I am trying to perform a simulation of CAL-B substrate. I added parameters of the substrate as instructed here: http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field When I run pdb2gmx in obtained .gro file, 3 bonds (P-B, P-CT and P-CA) break. The only bond with P that stays intact is with OS. I visualised PDB and gro files in VMD, when loading gro file, it says there are 4 fragments of the molecule loaded. Command used: pdb2gmx -f sub.pdb -o sub.gro -p sub.top. It ends with information about the topology being written successfully. How can I resolve this issue and keep the substrate in one piece?
Greetings, Ewa ____ PDB file goes as follows: HETATM 1 P1 PB1 A 318 -3.840 -9.371 7.084 P HETATM 2 B PB1 A 318 -5.264 -8.247 7.685 B HETATM 3 OS1 PB1 A 318 -3.548 -9.380 5.490 O HETATM 4 CT3 PB1 A 318 -3.954 -8.381 4.607 C HETATM 5 CT4 PB1 A 318 -2.929 -8.335 3.485 C HETATM 6 CT2 PB1 A 318 -5.314 -8.789 4.074 C HETATM 7 CA1 PB1 A 318 -3.951 -11.129 7.544 C HETATM 8 CA6 PB1 A 318 -3.323 -11.623 8.705 C HETATM 9 CA5 PB1 A 318 -3.410 -12.987 9.041 C HETATM 10 CA4 PB1 A 318 -4.132 -13.870 8.220 C HETATM 11 CA3 PB1 A 318 -4.769 -13.388 7.065 C HETATM 12 CA2 PB1 A 318 -4.678 -12.025 6.733 C HETATM 13 CT5 PB1 A 318 -2.152 -8.739 7.577 C HETATM 14 OS2 PB1 A 318 -1.867 -7.580 6.802 O HETATM 15 C PB1 A 318 -0.737 -6.824 6.943 C HETATM 16 O2 PB1 A 318 -0.688 -5.748 6.353 O HETATM 17 CT1 PB1 A 318 0.408 -7.314 7.805 C HETATM 18 HB1 PB1 A 318 -4.815 -7.367 8.380 H HETATM 19 HB2 PB1 A 318 -5.834 -7.750 6.739 H HETATM 20 HB3 PB1 A 318 -6.048 -8.904 8.334 H HETATM 21 H13 PB1 A 318 -4.001 -7.410 5.101 H HETATM 22 HC9 PB1 A 318 -1.930 -8.277 3.914 H HETATM 23 HC8 PB1 A 318 -3.013 -9.235 2.881 H HETATM 24 HC7 PB1 A 318 -3.097 -7.454 2.871 H HETATM 25 HC6 PB1 A 318 -5.307 -9.845 3.821 H HETATM 26 HC5 PB1 A 318 -5.519 -8.209 3.186 H HETATM 27 HC4 PB1 A 318 -6.083 -8.605 4.822 H HETATM 28 HA1 PB1 A 318 -2.759 -10.961 9.346 H HETATM 29 HA2 PB1 A 318 -2.914 -13.358 9.926 H HETATM 30 HA3 PB1 A 318 -4.193 -14.919 8.472 H HETATM 31 HA4 PB1 A 318 -5.325 -14.064 6.430 H HETATM 32 HA5 PB1 A 318 -5.166 -11.661 5.840 H HETATM 33 H12 PB1 A 318 -1.404 -9.510 7.398 H HETATM 34 H11 PB1 A 318 -2.145 -8.482 8.634 H HETATM 35 HC2 PB1 A 318 1.253 -6.646 7.661 H And the gro file: HETATM 1 P1 PB1 A 318 -3.840 -9.371 7.084 P HETATM 2 B PB1 A 318 -5.264 -8.247 7.685 B HETATM 3 OS1 PB1 A 318 -3.548 -9.380 5.490 O HETATM 4 CT3 PB1 A 318 -3.954 -8.381 4.607 C HETATM 5 CT4 PB1 A 318 -2.929 -8.335 3.485 C HETATM 6 CT2 PB1 A 318 -5.314 -8.789 4.074 C HETATM 7 CA1 PB1 A 318 -3.951 -11.129 7.544 C HETATM 8 CA6 PB1 A 318 -3.323 -11.623 8.705 C HETATM 9 CA5 PB1 A 318 -3.410 -12.987 9.041 C HETATM 10 CA4 PB1 A 318 -4.132 -13.870 8.220 C HETATM 11 CA3 PB1 A 318 -4.769 -13.388 7.065 C HETATM 12 CA2 PB1 A 318 -4.678 -12.025 6.733 C HETATM 13 CT5 PB1 A 318 -2.152 -8.739 7.577 C HETATM 14 OS2 PB1 A 318 -1.867 -7.580 6.802 O HETATM 15 C PB1 A 318 -0.737 -6.824 6.943 C HETATM 16 O2 PB1 A 318 -0.688 -5.748 6.353 O HETATM 17 CT1 PB1 A 318 0.408 -7.314 7.805 C HETATM 18 HB1 PB1 A 318 -4.815 -7.367 8.380 H HETATM 19 HB2 PB1 A 318 -5.834 -7.750 6.739 H HETATM 20 HB3 PB1 A 318 -6.048 -8.904 8.334 H HETATM 21 H13 PB1 A 318 -4.001 -7.410 5.101 H HETATM 22 HC9 PB1 A 318 -1.930 -8.277 3.914 H HETATM 23 HC8 PB1 A 318 -3.013 -9.235 2.881 H HETATM 24 HC7 PB1 A 318 -3.097 -7.454 2.871 H HETATM 25 HC6 PB1 A 318 -5.307 -9.845 3.821 H HETATM 26 HC5 PB1 A 318 -5.519 -8.209 3.186 H HETATM 27 HC4 PB1 A 318 -6.083 -8.605 4.822 H HETATM 28 HA1 PB1 A 318 -2.759 -10.961 9.346 H HETATM 29 HA2 PB1 A 318 -2.914 -13.358 9.926 H HETATM 30 HA3 PB1 A 318 -4.193 -14.919 8.472 H HETATM 31 HA4 PB1 A 318 -5.325 -14.064 6.430 H HETATM 32 HA5 PB1 A 318 -5.166 -11.661 5.840 H HETATM 33 H12 PB1 A 318 -1.404 -9.510 7.398 H HETATM 34 H11 PB1 A 318 -2.145 -8.482 8.634 H HETATM 35 HC2 PB1 A 318 1.253 -6.646 7.661 H -- 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
