[gmx-users] Need protein-ligand free energy calculation tutorial

[Naga Sundar]

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
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Re: [gmx-users] Stopping protein jumping inside box

[Naga Sundar]

Hi
 Plz try  -pbc nojump option...It may work

On Wed, Feb 13, 2013 at 5:29 AM, 라지브간디  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.
>
>
>
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[gmx-users] How to analysis 10 ns from 20 ns simulation

[Naga Sundar]

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

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Re: [gmx-users] Regarding append the run

[naga sundar]

Thanks justin got it...


On Wed, Oct 3, 2012 at 4:10 AM, Justin Lemkul  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/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==**==
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[gmx-users] Regarding append the run

[naga sundar]

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.



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Re: [gmx-users] xmgrace graphs

[naga sundar]

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  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
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Re: [gmx-users] Regarding RMSD analysis result

[naga sundar]

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
>>
>>
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Re: [gmx-users] Regarding RMSD analysis result

[naga sundar]

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 wrote:

> 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 
>
> > 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  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 
> > >> An: Discussion list for GROMACS users 
> > >> 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 
> 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

Re: [gmx-users] Regarding RMSD analysis result

[naga sundar]

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  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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N.NagaSundaram
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[gmx-users] Regarding RMSD analysis result

[naga sundar]

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
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Re: [gmx-users] Residue 'UNK' not found in residue topology database

[naga sundar]

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  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_database
>
> http://www.gromacs.org/**Documentation/How-tos/**Parameterization
>
> http://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/justin
>
> ==**==
>
> --
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[gmx-users] Regarding RMSD graph nalysis

[naga sundar]

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.
-- 
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