[gmx-users] parameters for Glucose-6-phosphate
Justin Lemkul
jalemkul at vt.edu
Fri Apr 29 18:13:06 CEST 2016
On 4/29/16 12:08 PM, Francesco Carbone wrote:
> Good afternoon,
>
> I'd like to run a dynamics with a protein (2bhl.pdb) and its substrate
> (Glucose-6-phosphate ) to observe how mutants affects the binding.
>
> Following Justin tutorial (thank you Justing for providing it), I use
> PRODRG to generate the topology for G6P and I then included in the protein
> topology.
>
> ; Include ligand topology
> #include "bg6.itp"
>
> BG6 1
>
> The problem that I'm having is a mismatch between the number of atoms in
> the coordinated and the topology once I try to add ions to the system.
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 226651)
> does not match topology (topol.top, 226644)
>
> THis should be connected with a discrepancy between ligand.pdb and
> ligand.itp, which have 20 and 27 atoms respectively.
>
> I tried to remove from the ligand.pdb the 7 atoms that do not have a
> counterpart in ligand.itp, but I always get a mismatch:
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 226663)
> does not match topology (topol.top, 226642)
>
> How can I fix this?
> below I pasted the pdb and itp files for the Glucose-6-phosphate
>
Your coordinate file includes all hydrogens, the topology does not (because
GROMOS FF are united-atom). So you can't use an all-atom coordinate set with a
united-atom topology.
Hopefully you'll investigate the suitability of the PRODRG topology before
actually spending time running a large simulation with it. The raw topologies
are never accurate (I linked my paper earlier today in another thread).
-Justin
> Thank you,
>
> Francesco
>
> ------------------ begin FILES ------------------
>
> PRODRG COORDS
> 27
> 1BG6 O1P 1 0.311 12.421 1.455
> 1BG6 P 2 0.384 12.355 1.345
> 1BG6 O2P 3 0.515 12.411 1.305
> 1BG6 O3P 4 0.376 12.208 1.349
> 1BG6 O6 5 0.295 12.402 1.219
> 1BG6 C6 6 0.153 12.391 1.232
> 1BG6 H61 7 0.123 12.288 1.211
> 1BG6 H62 8 0.128 12.426 1.332
> 1BG6 C5 9 0.082 12.483 1.136
> 1BG6 H5 10 0.096 12.586 1.170
> 1BG6 O5 11 0.146 12.465 1.008
> 1BG6 C1 12 0.090 12.551 0.908
> 1BG6 H11 13 0.105 12.655 0.938
> 1BG6 O1 14 0.155 12.529 0.787
> 1BG6 H12 15 0.141 12.434 0.759
> 1BG6 C2 16 -0.058 12.528 0.892
> 1BG6 H21 17 -0.075 12.425 0.861
> 1BG6 O2 18 -0.109 12.617 0.794
> 1BG6 H22 19 -0.094 12.712 0.823
> 1BG6 C3 20 -0.127 12.551 1.026
> 1BG6 H31 21 -0.108 12.653 1.059
> 1BG6 O3 22 -0.268 12.529 1.014
> 1BG6 H32 23 -0.285 12.435 0.983
> 1BG6 C4 24 -0.067 12.454 1.127
> 1BG6 H41 25 -0.081 12.352 1.092
> 1BG6 O4 26 -0.127 12.472 1.254
> 1BG6 H42 27 -0.113 12.567 1.284
> 0.95014 0.95014 0.95014
>
>
> ;
> ;
> ; This file was generated by PRODRG version AA100323.0717
> ; PRODRG written/copyrighted by Daan van Aalten
> ; and Alexander Schuettelkopf
> ;
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> ;
> ; When using this software in a publication, cite:
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> ; PRODRG - a tool for high-throughput crystallography
> ; of protein-ligand complexes.
> ; Acta Crystallogr. D60, 1355--1363.
> ;
> ;
>
> [ moleculetype ]
> ; Name nrexcl
> BG6 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OM 1 BG6 O1P 1 -0.715 15.9994
> 2 P 1 BG6 P 1 1.318 30.9738
> 3 OM 1 BG6 O2P 1 -0.714 15.9994
> 4 OM 1 BG6 O3P 1 -0.714 15.9994
> 5 OA 1 BG6 O6 1 -0.197 15.9994
> 6 CH2 1 BG6 C6 1 0.022 14.0270
> 7 CH1 1 BG6 C5 2 0.195 13.0190
> 8 OA 1 BG6 O5 2 -0.195 15.9994
> 9 CH1 1 BG6 C1 2 0.195 13.0190
> 10 OA 1 BG6 O1 2 -0.203 15.9994
> 11 H 1 BG6 H12 2 0.008 1.0080
> 12 CH1 1 BG6 C2 3 0.146 13.0190
> 13 OA 1 BG6 O2 3 -0.156 15.9994
> 14 H 1 BG6 H22 3 0.010 1.0080
> 15 CH1 1 BG6 C3 3 0.146 13.0190
> 16 OA 1 BG6 O3 3 -0.156 15.9994
> 17 H 1 BG6 H32 3 0.010 1.0080
> 18 CH1 1 BG6 C4 4 0.146 13.0190
> 19 OA 1 BG6 O4 4 -0.156 15.9994
> 20 H 1 BG6 H42 4 0.010 1.0080
>
> [ bonds ]
> ; ai aj fu c0, c1, ...
> 2 1 2 0.148 8600000.0 0.148 8600000.0 ; P O1P
> 2 3 2 0.148 8600000.0 0.148 8600000.0 ; P O2P
> 2 4 2 0.148 8600000.0 0.148 8600000.0 ; P O3P
> 2 5 2 0.161 4840000.0 0.161 4840000.0 ; P O6
> 6 5 2 0.143 8180000.0 0.143 8180000.0 ; C6 O6
> 7 6 2 0.153 7150000.0 0.153 7150000.0 ; C5 C6
> 7 8 2 0.144 6100000.0 0.144 6100000.0 ; C5 O5
> 7 18 2 0.152 5430000.0 0.152 5430000.0 ; C5 C4
> 9 8 2 0.144 6100000.0 0.144 6100000.0 ; C1 O5
> 9 10 2 0.144 6100000.0 0.144 6100000.0 ; C1 O1
> 9 12 2 0.152 5430000.0 0.152 5430000.0 ; C1 C2
> 10 11 2 0.100 15700000.0 0.100 15700000.0 ; O1 H12
> 12 13 2 0.144 6100000.0 0.144 6100000.0 ; C2 O2
> 12 15 2 0.152 5430000.0 0.152 5430000.0 ; C2 C3
> 13 14 2 0.100 15700000.0 0.100 15700000.0 ; O2 H22
> 15 16 2 0.144 6100000.0 0.144 6100000.0 ; C3 O3
> 15 18 2 0.152 5430000.0 0.152 5430000.0 ; C3 C4
> 16 17 2 0.100 15700000.0 0.100 15700000.0 ; O3 H32
> 18 19 2 0.144 6100000.0 0.144 6100000.0 ; C4 O4
> 19 20 2 0.100 15700000.0 0.100 15700000.0 ; O4 H42
>
> [ pairs ]
> ; ai aj fu c0, c1, ...
> 1 6 1 ; O1P C6
> 2 7 1 ; P C5
> 3 6 1 ; O2P C6
> 4 6 1 ; O3P C6
> 5 8 1 ; O6 O5
> 5 18 1 ; O6 C4
> 6 9 1 ; C6 C1
> 6 15 1 ; C6 C3
> 6 19 1 ; C6 O4
> 7 10 1 ; C5 O1
> 7 12 1 ; C5 C2
> 7 16 1 ; C5 O3
> 7 20 1 ; C5 H42
> 8 11 1 ; O5 H12
> 8 13 1 ; O5 O2
> 8 15 1 ; O5 C3
> 8 19 1 ; O5 O4
> 9 14 1 ; C1 H22
> 9 16 1 ; C1 O3
> 9 18 1 ; C1 C4
> 10 13 1 ; O1 O2
> 10 15 1 ; O1 C3
> 11 12 1 ; H12 C2
> 12 17 1 ; C2 H32
> 12 19 1 ; C2 O4
> 13 16 1 ; O2 O3
> 13 18 1 ; O2 C4
> 14 15 1 ; H22 C3
> 15 20 1 ; C3 H42
> 16 19 1 ; O3 O4
> 17 18 1 ; H32 C4
>
> [ angles ]
> ; ai aj ak fu c0, c1, ...
> 1 2 3 2 120.0 780.0 120.0 780.0 ; O1P P
> O2P
> 1 2 4 2 120.0 780.0 120.0 780.0 ; O1P P
> O3P
> 1 2 5 2 109.6 450.0 109.6 450.0 ; O1P P
> O6
> 3 2 4 2 120.0 780.0 120.0 780.0 ; O2P P
> O3P
> 3 2 5 2 109.6 450.0 109.6 450.0 ; O2P P
> O6
> 4 2 5 2 109.6 450.0 109.6 450.0 ; O3P P
> O6
> 2 5 6 2 120.0 530.0 120.0 530.0 ; P O6
> C6
> 5 6 7 2 109.5 520.0 109.5 520.0 ; O6 C6
> C5
> 6 7 8 2 109.5 320.0 109.5 320.0 ; C6 C5
> O5
> 6 7 18 2 109.5 520.0 109.5 520.0 ; C6 C5
> C4
> 8 7 18 2 109.5 520.0 109.5 520.0 ; O5 C5
> C4
> 7 8 9 2 109.5 380.0 109.5 380.0 ; C5 O5
> C1
> 8 9 10 2 109.5 320.0 109.5 320.0 ; O5 C1
> O1
> 8 9 12 2 109.5 520.0 109.5 520.0 ; O5 C1
> C2
> 10 9 12 2 109.5 520.0 109.5 520.0 ; O1 C1
> C2
> 9 10 11 2 109.5 450.0 109.5 450.0 ; C1 O1
> H12
> 9 12 13 2 109.5 520.0 109.5 520.0 ; C1 C2
> O2
> 9 12 15 2 109.5 520.0 109.5 520.0 ; C1 C2
> C3
> 13 12 15 2 109.5 520.0 109.5 520.0 ; O2 C2
> C3
> 12 13 14 2 109.5 450.0 109.5 450.0 ; C2 O2
> H22
> 12 15 16 2 109.5 520.0 109.5 520.0 ; C2 C3
> O3
> 12 15 18 2 109.5 520.0 109.5 520.0 ; C2 C3
> C4
> 16 15 18 2 109.5 520.0 109.5 520.0 ; O3 C3
> C4
> 15 16 17 2 109.5 450.0 109.5 450.0 ; C3 O3
> H32
> 7 18 15 2 109.5 520.0 109.5 520.0 ; C5 C4
> C3
> 7 18 19 2 109.5 520.0 109.5 520.0 ; C5 C4
> O4
> 15 18 19 2 109.5 520.0 109.5 520.0 ; C3 C4
> O4
> 18 19 20 2 109.5 450.0 109.5 450.0 ; C4 O4
> H42
>
> [ dihedrals ]
> ; ai aj ak al fu c0, c1, m, ...
> 2 1 4 3 2 35.3 334.8 35.3 334.8 ; imp P O1P
> O3P O2P
> 7 6 18 8 2 35.3 334.8 35.3 334.8 ; imp C5 C6
> C4 O5
> 9 8 12 10 2 35.3 334.8 35.3 334.8 ; imp C1 O5
> C2 O1
> 12 9 13 15 2 35.3 334.8 35.3 334.8 ; imp C2 C1
> O2 C3
> 15 12 18 16 2 35.3 334.8 35.3 334.8 ; imp C3 C2
> C4 O3
> 18 19 7 15 2 35.3 334.8 35.3 334.8 ; imp C4 O4
> C5 C3
> 6 5 2 1 1 0.0 3.1 2 0.0 3.1 2 ; dih C6 O6
> P O1P
> 7 6 5 2 1 0.0 1.3 3 0.0 1.3 3 ; dih C5 C6
> O6 P
> 18 7 6 5 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C5
> C6 O6
> 6 7 8 9 1 0.0 3.8 3 0.0 3.8 3 ; dih C6 C5
> O5 C1
> 19 18 7 6 1 0.0 5.9 3 0.0 5.9 3 ; dih O4 C4
> C5 C6
> 12 9 8 7 1 0.0 3.8 3 0.0 3.8 3 ; dih C2 C1
> O5 C5
> 8 9 10 11 1 0.0 1.3 3 0.0 1.3 3 ; dih O5 C1
> O1 H12
> 15 12 9 8 1 0.0 5.9 3 0.0 5.9 3 ; dih C3 C2
> C1 O5
> 9 12 13 14 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2
> O2 H22
> 18 15 12 9 1 0.0 5.9 3 0.0 5.9 3 ; dih C4 C3
> C2 C1
> 12 15 16 17 1 0.0 1.3 3 0.0 1.3 3 ; dih C2 C3
> O3 H32
> 19 18 15 12 1 0.0 5.9 3 0.0 5.9 3 ; dih O4 C4
> C3 C2
> 7 18 19 20 1 0.0 1.3 3 0.0 1.3 3 ; dih C5 C4
> O4 H42
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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