[gmx-users] pdb2gmx breaking bonds
Ewa Brylska
evunaa at gmail.com
Thu Aug 29 11:38:42 CEST 2013
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
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