[gmx-users] Need protein-ligand free energy calculation tutorial
Dear Gromacs users -- Iam trying to perform free energy calculation for protein-ligand complex. --Can any one plz suggess an appropriate tutorial to be follow to perform this analysis -- Thanks Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Stopping protein jumping inside box
Hi Plz try -pbc nojump option...It may work On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx users, I need to stop my protein jumping inside box. I have used -pbc mol -ur compact -center command too but still the protein gets moving from one place to other. Could you please suggest me how to make the protein to stop in one place ? Moreover, its protein with their ligand. Thnx. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] How to analysis 10 ns from 20 ns simulation
Dear users I performed 20 ns simulation for protein complex. After 10 ns only my system obtained equilibration state . I would like to analyze last 10 ns from the trajectory file.I got problem to generate last 10 ns xtc file from the 20 ns trr file. so, plz help me to sort out this problem -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding append the run
Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. What should be the problem.I need to append my run. -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding append the run
Thanks justin got it... On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/3/12 6:10 AM, naga sundar wrote: Dear friends Unfortunately my MD run got stopped. While i tried to append the run with command line mdrun -s fws_md.tpr -cp state.cpt -append, its not get appending, its again get restart. -cp is not a valid option. What you want is -cpi in your command line. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] xmgrace graphs
Dear Pramod use the command xmgrace -nxy file1.xvg file2.xvg Instead of file1 and file2 use ur file name. On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote: Dear Gromacs users, I am trying to find inter atomic distances between ligand atoms and protein residues using Gromacs commands and could generate individual xvg files, but could not figure out how to merge or show all the xvg files in one graph using xmgrace. Cold you please suggest? Thanks and Regards, Pramod -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
Dear justin
http://rmsdnagasundaram.blogspot.in/. This is the link to
my rmsd graph. Plz check it once and suggest me.
Thanks
On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım ahmedo...@gmail.comwrote:
Dear Tsjerk,
You said RMSD's above 1 nm are suspect, towards 2 highly likely not
correct. What is the physical/biological/chemical meaning of what you say?
Greetings
2012/9/24 Tsjerk Wassenaar tsje...@gmail.com
Hi,
RMSD's above 1 nm are suspect, towards 2 highly likely not correct.
You have to make sure that the molecule is made whole before doing
RMSD analysis.
Cheers,
Tsjerk
On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
You can also just quickly visualize it in VMD and see if anything your
looking at is not centred properly. If it isnt you just have to centre
it.
Stephan
Original-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I
followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So its confirmed that
nothing
wrong with periodic conditions. Since all the three mutations were
having
high clinical significance, we assuming mutation is the only reason
for
this abnormal RMSD behavior. Sudden big increase in the RMSD was
observed
in previous mutational MD studies.
http://www.sciencedirect.com/science/article/pii/S0006291X08020792.
Overall, all the factors are supporting our results. So shall we take
this
RMSD analysis as good result . Even after repeating the 20 ns MD
simulation
two times i got the same results.
On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu
wrote:
On 9/24/12 6:24 AM, naga sundar wrote:
Dear gromacs users
We performed MD simulation analysis for native and
mutant
models of protein-protein complexes. From 20 ns simulation
trajectory,
we
generated RMSD graph for one native and three mutant complexes. For
native
complex in the entire simulation period, we observed a constant
RMSD
(~0.15 to ~ 0.25 nm). But, three mutant complexes
showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We
analysed
all the 3D structure's in the fluctuated areas observed destruction
of
protein complexes.
All the three mutants were already experimentally analyzed and
reported
that they are involved in the destruction of protein-protein
interactions.
Query 1: What may be the reason for sudden rise and fall of the
RMSD
values
in mutant complexes. We are assume its because of the involvement
of
mutation.
Query 2: Is there may any other reasons for drastic fluctuation in
the
RMSD
Query 3: Observed results are rite.
Here iam attaching the RMSD graph for your observation.
Attachments to the list do not work. You will have to post a link
to
a
file sharing site if you wish to share an image.
Such jumps in RMSD are very suspect. Since you are dealing with
protein-protein complexes, accounting for periodicity can be very
challenging. Have you properly fit the trajectory such that your
protein
subunits are not jumping across periodic boundaries? If they are,
then
your results are nothing more than an artifact. If they are not,
then
you
have something more interesting, but a tenfold increase in RMSD is
very
peculiar.
-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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
==**==
--
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--
Regards
N.NagaSundaram
--
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http://lists.gromacs.org
Re: [gmx-users] Regarding RMSD analysis result
Dear Felipe Thanks for ur reply. The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. of-course this is not the first MD run for these native and mutant complexes. I run twice and got the same results. I want know this kind of RMSD is rite r wrong?.. On Tue, Sep 25, 2012 at 12:45 AM, Felipe Pineda, PhD luis.pinedadecas...@lnu.se wrote: It looks for me like the known pbc effect others already pointed to. If you have just a protein-ligand complex (+ water and counterions of course) it's relatively easy to manually (a piece of code would do it) bring the ligand to the correct position in the frames showing an abnormally high value by subtracting half the x/y dimension of the box from its coordinates and re-calculate the rmsd , but I think trjconv would do it as well. Felipe On 09/25/2012 09:22 AM, naga sundar wrote: Dear justin http://rmsdnagasundaram.**blogspot.in/http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me. Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding RMSD analysis result
Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Regarding RMSD analysis result
Dear justin Thanks for ur suggestions While speaking about periodic conditions, I followed the similar condition for both native and mutant complexes. For native complexes not any big deviation was observed. So its confirmed that nothing wrong with periodic conditions. Since all the three mutations were having high clinical significance, we assuming mutation is the only reason for this abnormal RMSD behavior. Sudden big increase in the RMSD was observed in previous mutational MD studies. http://www.sciencedirect.com/science/article/pii/S0006291X08020792. Overall, all the factors are supporting our results. So shall we take this RMSD analysis as good result . Even after repeating the 20 ns MD simulation two times i got the same results. On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/24/12 6:24 AM, naga sundar wrote: Dear gromacs users We performed MD simulation analysis for native and mutant models of protein-protein complexes. From 20 ns simulation trajectory, we generated RMSD graph for one native and three mutant complexes. For native complex in the entire simulation period, we observed a constant RMSD (~0.15 to ~ 0.25 nm). But, three mutant complexes showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We analysed all the 3D structure's in the fluctuated areas observed destruction of protein complexes. All the three mutants were already experimentally analyzed and reported that they are involved in the destruction of protein-protein interactions. Query 1: What may be the reason for sudden rise and fall of the RMSD values in mutant complexes. We are assume its because of the involvement of mutation. Query 2: Is there may any other reasons for drastic fluctuation in the RMSD Query 3: Observed results are rite. Here iam attaching the RMSD graph for your observation. Attachments to the list do not work. You will have to post a link to a file sharing site if you wish to share an image. Such jumps in RMSD are very suspect. Since you are dealing with protein-protein complexes, accounting for periodicity can be very challenging. Have you properly fit the trajectory such that your protein subunits are not jumping across periodic boundaries? If they are, then your results are nothing more than an artifact. If they are not, then you have something more interesting, but a tenfold increase in RMSD is very peculiar. -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Residue 'UNK' not found in residue topology database
Dear simone I think so u r using the same pr.mdp and md.mdp files what u created initially. So open both the mdp files replace DRG with UNK and the try sure it will work out. On Tue, Sep 18, 2012 at 9:44 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/18/12 12:42 PM, SIMONE BROGI wrote: Dear gromacs user, I have a complex generated by docking calculation and I would perform a MD by gromacs. I have a problem with ligand atoms. In the pdb file the ligand appears as UNK and if I process this file in order to start simulation I receive this messagge error: Residue 'UNK' not found in residue topology database this part of file concerning ligand and it is not a residue. In order to fix this problem can I replace the UNK with another tag that is Known in topology database for a ligand??? or How can I fix this error??? Most ligands are not part of existing force fields. Please consult the following: http://www.gromacs.org/**Documentation/Errors#Residue_'** XXX'_not_found_in_residue_**topology_databasehttp://www.gromacs.org/Documentation/Errors#Residue_%27XXX%27_not_found_in_residue_topology_database http://www.gromacs.org/**Documentation/How-tos/**Parameterizationhttp://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/**Documentation/How-tos/Adding_** a_Residue_to_a_Force_Fieldhttp://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -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/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Regarding RMSD graph nalysis
Dear gromacs users I run 20 ns MD simulation for protein mutant complexes. In RMSD analysis at ~9 ns sudden increase in the deviation was observed from 0.2 nm to 1.7 nm and immediate fall was observed. I rerun the 20 ns simulation for the same molecule with same procedure. While analyzing the RMSD sudden increase in the deviation was observed (0.2 nm to 1.7 nm) at the simulation period of ~12 ns. So i want to know the reason For sudden rise and fall in RMSD values. Next, in first MD run this deviation was observed at ~9 ns (0.2 nm to 1.7 nm) but while rerun the molecule with same procedure this deviation was observed at ~12 ns. -- Regards N.NagaSundaram -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
