[gmx-users] Protein-ligand - genion error
Ankita naithani
ankitanaithani at gmail.com
Fri Aug 10 19:52:52 CEST 2012
Hi Justin,
Thank you so much for your reply. It really helped me a lot.
I think I have managed to clear this step.
Thanks once again.
Best Wishes,
On Fri, Aug 10, 2012 at 6:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Only plain text messages are allowed!
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
Ankita Naithani
More information about the gromacs.org_gmx-users
mailing list