[gmx-users] pdb2gmx breaking bonds
Justin Lemkul
jalemkul at vt.edu
Thu Aug 29 13:59:06 CEST 2013
On 8/29/13 5:38 AM, Ewa Brylska wrote:
> 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?
>
First and foremost, please consider the following:
http://www.gromacs.org/Downloads/Related_Software/Visualization_Software#Topology_bonds_vs_Rendered_bonds
What VMD thinks about the bonded structure is completely irrelevant to Gromacs.
Look in the text of the topology - are the bonds there? pdb2gmx will do
exactly what you tell it.
-Justin
> 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
>
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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