[gmx-users] Protein-ligand - genion error

[Justin Lemkul]

On 8/10/12 1:26 PM, Ankita naithani wrote:
> Hi Justin,
>
> Thank you for your response.
>
> The co-ordinate file that you have mentioned. Is it the one obtained
> after running pdb2gmx step or the one after running genbox step?
>
> Also, I am putting few outputs for your referral..
>
> My co-ordinate file after building topology and incorporating my
> ligand topology, looks like this:
>
> ----
> 498GLU     O119587   0.147   1.260   4.509
>    498GLU     O219588   0.017   1.177   4.669
>    501HOH     OW19589  -3.995   3.677  -0.161
> ----
> 2139HOH    HW223341   0.013   0.653   1.232
>      1FDP  O1P      1  -0.608   6.909  -0.874
>      1FDP  P1       2  -0.474   6.859  -0.904
> -----
> 1FDP  O4P     23   0.758   0.467   2.079
>      1ATP  O1G      1  -3.672   4.724  -0.730
>      1ATP  PG       2  -3.697   4.678  -0.871
> -------
> 1ATP  H62     36   3.986   0.936   1.930
>      1ATP  H61     37   4.112   0.822   1.964
>      1OXL  O1       1  -3.442   4.377  -0.541
>      1OXL  C1       2  -3.431   4.424  -0.655
>
> My co-ordinate file after defining box looks like this:
>
> 498GLU      C19586  12.309   9.794   8.852
>    498GLU     O119587  12.411   9.858   8.823
>    498GLU     O219588  12.281   9.775   8.983
>    501HOH     OW19589   8.269  12.275   4.153
>    501HOH    HW119590   8.351  12.275   4.210
>    501HOH    HW219591   8.187  12.275   4.210
>    503HOH     OW19592  10.623  12.907   4.675
> ----------------
> 2139HOH    HW123340  12.195   9.170   5.661
>   2139HOH    HW223341  12.277   9.251   5.546
>      1FDP    O1P23342  11.656  15.507   3.440
>      1FDP     P123343  11.790  15.457   3.410
>      1FDP    O2P23344  11.857  15.521   3.280
>
>
> My co-ordinate file after solvation looks like this:
>
> 498GLU    OE219585  11.824   9.468   8.693
>    498GLU      C19586  12.309   9.794   8.852
>    498GLU     O119587  12.411   9.858   8.823
>    498GLU     O219588  12.281   9.775   8.983
>    501HOH     OW19589   8.269  12.275   4.153
>    501HOH    HW119590   8.351  12.275   4.210
> ----------
> 2139HOH    HW223341  12.277   9.251   5.546
>      1FDP    O1P23342  11.656  15.507   3.440
>      1FDP     P123343  11.790  15.457   3.410
> ------------
>
>   1FDP     O423604  15.520  10.331   5.622
>      1FDP     O223605  15.614  10.234   5.451
>      2SOL     OW23606   0.230   0.628   0.113
>      2SOL    HW123607   0.137   0.626   0.150
>      2SOL    HW223608   0.231   0.589   0.021
>      3SOL     OW23609   0.569   1.275   1.165
>      3SOL    HW123610   0.476   1.268   1.128
>      3SOL    HW223611   0.580   1.364   1.209
>      4SOL     OW23612   1.555   1.511   0.703
> -------------
>
> 91503SOL    HW198110  16.284  14.907  11.256
> 91503SOL    HW298111  16.159  14.910  11.360
> 91504SOL     OW98112  14.935  15.974  11.472
> 91504SOL    HW198113  15.034  15.963  11.463
> 91504SOL    HW298114  14.895  15.888  11.504
>
> ----------------------------------
>
> and my topology file has following:
>
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     1
> Protein_chain_B     1
> Protein_chain_C     1
> Protein_chain_D     1
> SOL               167
> SOL               379
> SOL               305
> SOL               400
> FDP		    4
> ATP		    4
> OXL		    4
> SOL             91503
>
>
> I think you are talking about the co-ordinate file obtained after
> solvation, right?
>

Yes.

> I do notice that FDp is between HOH and SOL but if I remove FDP, my
> ligand will be removed.
>

I didn't say to remove it, I said to change its position within the coordinate 
file.  Right now, you have FDP, ATP, and OXL breaking up your SOL section.  You 
can't do that - all the SOL entries need to be continuous in the coordinate and 
topology files.

> The second thing I noticed is that I had put the information for all
> the three ligands i.e. FDP,ATP and OXL but subsequently, I find that
> only FDP is present in these files and not ATP and OXL.
>

Then you need to figure out at which point they got deleted and re-add them, 
otherwise you'll have plenty of more problems later on.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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