hi justin,<br><br>as u said i understand that there is inconsistency in the charges and charge groups of PRODRG server itself.<br>can u suggest me any other softwares that i can rely on for this work.<br><br>Thanking you.<br>
<br><div class="gmail_quote">On Tue, Nov 15, 2011 at 7:48 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Today's Topics:<br>
<br>
1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul)<br>
2. RMSD (shahid nayeem)<br>
3. Problem during GROMACS 4.5.5 installation (sai nitin)<br>
4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul)<br>
5. Re: RMSD (Gianluca Santoni)<br>
6. Re: RMSD (<a href="mailto:felmerino@uchile.cl">felmerino@uchile.cl</a>)<br>
7. Re: Positive potential energy for TFE solvent (Harpreet Basra)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 15 Nov 2011 06:40:31 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC24FAF.5050704@vt.edu">4EC24FAF.5050704@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
arun kumar wrote:<br>
> Dear friends,<br>
><br>
> i had a problem while running the of protein-ligand complex simulation,<br>
> in which i have generated the ligand toplogy by using online Prodrg<br>
> server and iam using gromos 96.1froce field.<br>
><br>
> there was an note and an error during minimization<br>
><br>
> NOTE 2 [file trp.top]:<br>
> The largest charge group contains 15 atoms.<br>
> Since atoms only see each other when the centers of geometry of the charge<br>
> groups they belong to are within the cut-off distance, too large charge<br>
> groups can lead to serious cut-off artifacts.<br>
> For efficiency and accuracy, charge group should consist of a few atoms.<br>
> For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.<br>
><br>
> Analysing residue names:<br>
> There are: 223 Protein residues<br>
> There are: 1 Other residues<br>
> There are: 25853 Water residues<br>
> Analysing Protein...<br>
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting<br>
> into groups...<br>
> Number of degrees of freedom in T-Coupling group rest is 161838.00<br>
> Largest charge group radii for Van der Waals: 0.790, 0.356 nm<br>
> Largest charge group radii for Coulomb: 0.790, 0.399 nm<br>
><br>
> WARNING 1 [file em.mdp]:<br>
> The sum of the two largest charge group radii (1.188798) is larger than<br>
> rlist (1.000000)<br>
><br>
> i am using the mdp file the one that i copied from gromacs<br>
> protein-ligand tutorial<br>
><br>
> can any one please explain these errors so that i can go farward in my work.<br>
><br>
<br>
<a href="http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_%28X%29_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb" target="_blank">http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb</a><br>
<br>
> and i have a doubt, as there are other updated forcefields, how much<br>
> reliable is the gromos 96 ff....<br>
><br>
<br>
The problem is not the reliability of Gromos96, but the reliability of PRODRG.<br>
Please read the paper linked from<br>
<a href="http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips" target="_blank">http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips</a> to understand why<br>
you should almost certainly never use the charges and charge groups that PRODRG<br>
creates.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 15 Nov 2011 17:53:19 +0530<br>
From: shahid nayeem <<a href="mailto:msnayeem@gmail.com">msnayeem@gmail.com</a>><br>
Subject: [gmx-users] RMSD<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<CAB_3DJa8m-jooJb=<a href="mailto:CMSCMRds8jA-rzDM7GMDm%2BOKu7s7Qem8tA@mail.gmail.com">CMSCMRds8jA-rzDM7GMDm+OKu7s7Qem8tA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear all<br>
I am interested to get contour plot of residue RMSD vs time graph. I want<br>
to get the flexible and rigid regions of protein chain during simulation.<br>
g_rmsf does not gives me this plot.<br>
Please help<br>
shahid Nayeem<br>
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Message: 3<br>
Date: Tue, 15 Nov 2011 14:03:03 +0100<br>
From: sai nitin <<a href="mailto:sainitin7@gmail.com">sainitin7@gmail.com</a>><br>
Subject: [gmx-users] Problem during GROMACS 4.5.5 installation<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:CAGJtc4NWdF9A2V9T8eep1JMa%2Bs4KECOa6p8RNL6vNM_M7HQkAw@mail.gmail.com">CAGJtc4NWdF9A2V9T8eep1JMa+s4KECOa6p8RNL6vNM_M7HQkAw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi all,<br>
<br>
<br>
I just started learning molecular dynamics analysis of protein-ligand<br>
complexes to do this i downloaded GROMACS 4.5.5 and tried to install<br>
according to Manual instructions executed following commands..<br>
<br>
./configure<br>
make (when i executed this command it is showing following error *** No<br>
targets specified and no makefile found)<br>
<br>
Can any body help how to solved this...<br>
<br>
Thanks in advance<br>
--<br>
<br>
Sainitin D<br>
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<br>
Message: 4<br>
Date: Tue, 15 Nov 2011 08:13:40 -0500<br>
From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Problem during GROMACS 4.5.5 installation<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC26584.8060803@vt.edu">4EC26584.8060803@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
<br>
<br>
sai nitin wrote:<br>
> Hi all,<br>
><br>
><br>
> I just started learning molecular dynamics analysis of protein-ligand<br>
> complexes to do this i downloaded GROMACS 4.5.5 and tried to install<br>
> according to Manual instructions executed following commands..<br>
><br>
> ./configure<br>
> make (when i executed this command it is showing following error *** No<br>
> targets specified and no makefile found)<br>
><br>
<br>
Configuration failed. Simply specifying ./configure without any options is<br>
often insufficient. Please follow the installation guide online.<br>
<br>
-Justin<br>
<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Tue, 15 Nov 2011 21:18:16 +0800<br>
From: Gianluca Santoni <<a href="mailto:gianluca.santoni@ibs.fr">gianluca.santoni@ibs.fr</a>><br>
Subject: Re: [gmx-users] RMSD<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4EC26698.7000804@ibs.fr">4EC26698.7000804@ibs.fr</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 11/15/11 8:23 PM, shahid nayeem wrote:<br>
> Dear all<br>
> I am interested to get contour plot of residue RMSD vs time graph. I<br>
> want to get the flexible and rigid regions of protein chain during<br>
> simulation. g_rmsf does not gives me this plot.<br>
> Please help<br>
> shahid Nayeem<br>
><br>
><br>
><br>
Try g_rmsf -res , it could be useful, maybe.<br>
<br>
--<br>
Gianluca Santoni,<br>
Institut de Biologie Structurale<br>
41 rue Horowitz<br>
Grenoble<br>
_________________________________________________________<br>
Please avoid sending me Word or PowerPoint attachments.<br>
See <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
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<br>
Message: 6<br>
Date: Tue, 15 Nov 2011 10:32:16 -0300 (GMT-03:00)<br>
From: "<a href="mailto:felmerino@uchile.cl">felmerino@uchile.cl</a>" <<a href="mailto:felmerino@uchile.cl">felmerino@uchile.cl</a>><br>
Subject: Re: [gmx-users] RMSD<br>
To: <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID:<br>
<10450993.2631321363936014.JavaMail.defaultUser@defaultHost><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
<br>
In any case, if you really want to see flexibility then you need RMSF and not RMSD as the later will only tell you about how similar is the configuration of a sidechain compared to a reference frame. If that is still what you want i think VMD has a tool for that in the timeline plugin.<br>
<br>
<br>
<br>
regards<br>
<br>
<br>
<br>
Felipe<br>
----Mensaje original---- De: <a href="mailto:gianluca.santoni@ibs.fr">gianluca.santoni@ibs.fr</a> Fecha: 15-nov-2011 10:18 Para: "Discussion list for GROMACS users"<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>> Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote:<br>
Dear all<br>
I am interested to get contour plot of residue RMSD vs time graph. I want to get the flexible and rigid regions of protein chain during simulation. g_rmsf does not gives me this plot.<br>
Please help<br>
shahid Nayeem<br>
<br>
<br>
Try g_rmsf -res , it could be useful, maybe.<br>
--<br>
Gianluca Santoni,<br>
Institut de Biologie Structurale<br>
41 rue Horowitz<br>
Grenoble<br>
_________________________________________________________<br>
Please avoid sending me Word or PowerPoint attachments.<br>
See <a href="http://www.gnu.org/philosophy/no-word-attachments.html" target="_blank">http://www.gnu.org/philosophy/no-word-attachments.html</a><br>
<br>
<br>
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Message: 7<br>
Date: Tue, 15 Nov 2011 19:48:06 +0530<br>
From: Harpreet Basra <<a href="mailto:harpreetk.basra@gmail.com">harpreetk.basra@gmail.com</a>><br>
Subject: [gmx-users] Re: Positive potential energy for TFE solvent<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID:<br>
<<a href="mailto:CAEAiM5sSFLvHhe%2BZM1Z60T4b-BkuJ5VcPbEfza92g255qY27rA@mail.gmail.com">CAEAiM5sSFLvHhe+ZM1Z60T4b-BkuJ5VcPbEfza92g255qY27rA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Hi Mark,<br>
<br>
Thanks for the quick reply. But i have already done what u suggested.<br>
<br>
<br>
><br>
> On 15/11/2011 6:06 PM, Harpreet Basra wrote:<br>
> > Hi<br>
> > I am still stuck with same problem of obtaining positive potential<br>
> > energy.<br>
> > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote:<br>
> > >> Hi<br>
> > >><br>
> > >> I am trying to generate an equilibrated box of 216 TFE molecules.To<br>
> > >> generate the 216 TFE molecule box i performed following steps:<br>
> > ><br>
> > >A suggested workflow can be found here<br>
> > ><a href="http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation" target="_blank">http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation</a><br>
> > I have been following this link only.<br>
> > ><br>
> > ><br>
> > >> 1) I got the tfe.gro file and created a cubic box of edge length =<br>
> > >> 0.516 nm containing 1 TFE molecule (at its center), using the<br>
> > >> following command:<br>
> > >><br>
> > >>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516<br>
> > >> I chose this length because in the tfe.gro file dimensions of the TFE<br>
> > >> molecule are 0.516 0.516 0.516.<br>
> > ><br>
> > >That's not a good reason. Choose a volume and shape that makes sense for<br>
> > >your target density. Cubic probably doesn't make sense when a<br>
> > >rectangular shape is possible. Then you'll probably want to choose -nbox<br>
> > >differently later.<br>
> > I chose a rectangular box too. still i get a positive value for PE and<br>
> > moreover all the molecules move towards two opposite walls of the box.<br>
> > I am not sure that the way I am using the genconf command is the<br>
> > correct way. because I have tried every other possibility for not<br>
> > getting a positive potential, with no success. So here are my .gro<br>
> > file and the topology file for TFE.<br>
> > *****tfe.gro file*****<br>
> > 7<br>
> ><br>
> > 1TFE F1T 1 0.444 0.344 0.246<br>
> ><br>
> > 1TFE CT 2 0.334 0.245 0.246<br>
> ><br>
> > 1TFE F2T 3 0.350 0.160 0.364<br>
> ><br>
> > 1TFE F3T 4 0.350 0.160 0.127<br>
> ><br>
> > 1TFE CH2T 5 0.187 0.326 0.246<br>
> ><br>
> > 1TFE OT 6 0.075 0.220 0.246<br>
> ><br>
> > 1TFE HT 7 -0.019 0.266 0.246<br>
> ><br>
> > 0.49174 0.49174 0.49174<br>
> ><br>
> > ****topology file****<br>
> ><br>
> > [ moleculetype ]<br>
> ><br>
> > ; Name nrexcl<br>
> ><br>
> > TFE 3<br>
> ><br>
> > [ atoms ]<br>
> ><br>
> > ; nr type resnr resid atom cgnr charge mass<br>
> ><br>
> > 1 FTFE 1 TFE F1T 1 -0.170 18.9984<br>
> ><br>
> > 2 CTFE 1 TFE CT 1 0.452 12.0110<br>
> ><br>
> > 3 FTFE 1 TFE F2T 1 -0.170 18.9984<br>
> ><br>
> > 4 FTFE 1 TFE F3T 1 -0.170 18.9984<br>
> ><br>
> > 5 CHTFE 1 TFE CH2T 1 0.273 14.0270<br>
> ><br>
> > 6 OTFE 1 TFE OT 1 -0.625 15.9994<br>
> ><br>
> > 7 H 1 TFE HT 1 0.410 1.0080<br>
> ><br>
> > [ bonds ]<br>
> ><br>
> > ; ai aj fu c0, c1, ...<br>
> ><br>
> > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1<br>
> ><br>
> > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2<br>
> ><br>
> > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3<br>
> ><br>
> > 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2<br>
> ><br>
> > 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O<br>
> ><br>
> > 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H<br>
> ><br>
> > [ pairs ]<br>
> ><br>
> > ; ai aj fu c0, c1, ...<br>
> ><br>
> > 1 6 1 ; F1 O<br>
> ><br>
> > 2 7 1 ; C1 H<br>
> ><br>
> > 3 6 1 ; F2 O<br>
> ><br>
> > 4 6 1 ; F3 O<br>
> ><br>
> > [ angles ]<br>
> ><br>
> > ; ai aj ak fu c0, c1, ...<br>
> ><br>
> > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2<br>
> ><br>
> > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3<br>
> ><br>
> > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2<br>
> ><br>
> > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3<br>
> ><br>
> > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2<br>
> ><br>
> > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2<br>
> ><br>
> > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O<br>
> ><br>
> > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H<br>
> ><br>
> > [ dihedrals ]<br>
> ><br>
> > ; ai aj ak al fu c0, c1, m, ...<br>
> ><br>
> > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1<br>
> ><br>
> > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H<br>
> ><br>
> > and to construct a box of TFE solvent i took the tfe.gro file and<br>
> > replicated the TFE molecule by using<br>
> > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6<br>
> > can u plz suggest is it that I am using genconf in a wrong way that it<br>
> > is causing this problem? I am not sure how many molecules (-nbox<br>
> > option in genconf) should i keep in the box in order to get a mass<br>
> > density of 1383g/L for TFE.<br>
><br>
> That link says "Work out how much volume a single molecule would have in<br>
> the box of your chosen density and size. Useeditconf<br>
> <<a href="http://www.gromacs.org/editconf" target="_blank">http://www.gromacs.org/editconf</a>>to place a box of that size around your<br>
> single molecule." It does not seem to me that you have done this.<br>
><br>
> Mark<br>
><br>
<br>
I did place the *single molecule* in a box of size required to get a<br>
density of 1383 g/L. I also checked the density of the solvent box<br>
(containing 216 molecules after NVT equilibration for 200 ps) I constructed<br>
the average value comes out to be 1397 g/L with a std deviation of 30 g/L,<br>
thus it seems range. Moreover, the potential energy of this one molecule<br>
(tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on<br>
generating a solvent system with 216 TFE molecules the energy becomes<br>
(1.9E+04 kJ/mol).<br>
<br>
Harpreet<br>
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End of gmx-users Digest, Vol 91, Issue 104<br>
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</font></blockquote></div><br><br clear="all"><br>-- <br>Arun Kumar Somavarapu<br>Project-JRF<br><div>Dr. Prasanna's lab<br>TMC, ACTREC<br>Navi Mumbai-410210<br></div><br>