[gmx-users] Protein-ligand - genion error
Ankita naithani
ankitanaithani at gmail.com
Fri Aug 10 19:26:29 CEST 2012
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?
I do notice that FDp is between HOH and SOL but if I remove FDP, my
ligand will be removed.
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.
Please, could help me with both my problems.
On Fri, Aug 10, 2012 at 6:08 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/10/12 1:05 PM, Ankita naithani wrote:
>>
>> Dear All,
>>
>> I have been trying to perform simulation for a Protein and Ligand
>> complex. However, when I run genion, I get an error "The solvent group
>> SOL is not continuous: index[37530=23341, index[3754]=23606.
>>
>> I remember reading someone posting a similar problem and the solution
>> was provided, according to which we need to manipulate the co-ordinate
>> file and topology file. But, the problem is I really cannot understand
>> at the moment as to what exactly changes I should make in order to run
>> it and rectify this error. I would be really grateful if someone
>> could help me and let me know as to what exactly and how I need to
>> incorporate the changes. Also, the co-ordinate file, should the
>> changes be made to the one obtained after running the genbox step?
>>
>
> In the coordinate file, you'll find lines for SOL, then something else, then
> more SOL. Your SOL lines need to be continuous, so you have to cut out
> whatever is breaking the two solvent blocks, put it either before or after
> SOL, and then make sure the [molecules] section of the topology agrees with
> contents of the new coordinate file in terms of number of molecules and
> order of appearance.
>
> -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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--
Ankita Naithani
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