[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



More information about the gromacs.org_gmx-users mailing list