[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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