[gmx-users] parameters for Glucose-6-phosphate
Francesco Carbone
fra.carbone8 at gmail.com
Fri Apr 29 18:49:22 CEST 2016
Thank you for your reply Justin,
Of course I'll investigate the suitability of the PRODRG topology.
I was simply trying to see if I could quickly set up a simulation before
checking.
I thought that I was converting to united-atom conformation with pdb2gmx
when selecting the GROMOS ff option.
Francesco
On 29 April 2016 at 17:12, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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