hi justin, as u said i understand that there is inconsistency in the charges and charge groups of PRODRG server itself. can u suggest me any other softwares that i can rely on for this work.
Thanking you. On Tue, Nov 15, 2011 at 7:48 PM, <[email protected]> wrote: > Send gmx-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION (Justin A. Lemkul) > 2. RMSD (shahid nayeem) > 3. Problem during GROMACS 4.5.5 installation (sai nitin) > 4. Re: Problem during GROMACS 4.5.5 installation (Justin A. Lemkul) > 5. Re: RMSD (Gianluca Santoni) > 6. Re: RMSD ([email protected]) > 7. Re: Positive potential energy for TFE solvent (Harpreet Basra) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 15 Nov 2011 06:40:31 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] ERRORS IN PROTEIN-LIGAND COMPLEX SIMULATION > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > arun kumar wrote: > > Dear friends, > > > > i had a problem while running the of protein-ligand complex simulation, > > in which i have generated the ligand toplogy by using online Prodrg > > server and iam using gromos 96.1froce field. > > > > there was an note and an error during minimization > > > > NOTE 2 [file trp.top]: > > The largest charge group contains 15 atoms. > > Since atoms only see each other when the centers of geometry of the > charge > > groups they belong to are within the cut-off distance, too large charge > > groups can lead to serious cut-off artifacts. > > For efficiency and accuracy, charge group should consist of a few > atoms. > > For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. > > > > Analysing residue names: > > There are: 223 Protein residues > > There are: 1 Other residues > > There are: 25853 Water residues > > Analysing Protein... > > Analysing residues not classified as Protein/DNA/RNA/Water and splitting > > into groups... > > Number of degrees of freedom in T-Coupling group rest is 161838.00 > > Largest charge group radii for Van der Waals: 0.790, 0.356 nm > > Largest charge group radii for Coulomb: 0.790, 0.399 nm > > > > WARNING 1 [file em.mdp]: > > The sum of the two largest charge group radii (1.188798) is larger than > > rlist (1.000000) > > > > i am using the mdp file the one that i copied from gromacs > > protein-ligand tutorial > > > > can any one please explain these errors so that i can go farward in my > work. > > > > > http://www.gromacs.org/Documentation/Errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb > > > and i have a doubt, as there are other updated forcefields, how much > > reliable is the gromos 96 ff.... > > > > The problem is not the reliability of Gromos96, but the reliability of > PRODRG. > Please read the paper linked from > http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips to > understand why > you should almost certainly never use the charges and charge groups that > PRODRG > creates. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 2 > Date: Tue, 15 Nov 2011 17:53:19 +0530 > From: shahid nayeem <[email protected]> > Subject: [gmx-users] RMSD > To: Discussion list for GROMACS users <[email protected]> > Message-ID: > <CAB_3DJa8m-jooJb=cmscmrds8ja-rzdm7gmdm+oku7s7qem...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > 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. > Please help > shahid Nayeem > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/c99194fb/attachment-0001.html > > ------------------------------ > > Message: 3 > Date: Tue, 15 Nov 2011 14:03:03 +0100 > From: sai nitin <[email protected]> > Subject: [gmx-users] Problem during GROMACS 4.5.5 installation > To: [email protected] > Message-ID: > <cagjtc4nwdf9a2v9t8eep1jma+s4kecoa6p8rnl6vnm_m7hq...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi all, > > > I just started learning molecular dynamics analysis of protein-ligand > complexes to do this i downloaded GROMACS 4.5.5 and tried to install > according to Manual instructions executed following commands.. > > ./configure > make (when i executed this command it is showing following error *** No > targets specified and no makefile found) > > Can any body help how to solved this... > > Thanks in advance > -- > > Sainitin D > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/ab159056/attachment-0001.html > > ------------------------------ > > Message: 4 > Date: Tue, 15 Nov 2011 08:13:40 -0500 > From: "Justin A. Lemkul" <[email protected]> > Subject: Re: [gmx-users] Problem during GROMACS 4.5.5 installation > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > sai nitin wrote: > > Hi all, > > > > > > I just started learning molecular dynamics analysis of protein-ligand > > complexes to do this i downloaded GROMACS 4.5.5 and tried to install > > according to Manual instructions executed following commands.. > > > > ./configure > > make (when i executed this command it is showing following error *** No > > targets specified and no makefile found) > > > > Configuration failed. Simply specifying ./configure without any options is > often insufficient. Please follow the installation guide online. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > ------------------------------ > > Message: 5 > Date: Tue, 15 Nov 2011 21:18:16 +0800 > From: Gianluca Santoni <[email protected]> > Subject: Re: [gmx-users] RMSD > To: Discussion list for GROMACS users <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset="iso-8859-1" > > On 11/15/11 8:23 PM, shahid nayeem wrote: > > Dear all > > 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. > > Please help > > shahid Nayeem > > > > > > > Try g_rmsf -res , it could be useful, maybe. > > -- > Gianluca Santoni, > Institut de Biologie Structurale > 41 rue Horowitz > Grenoble > _________________________________________________________ > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/fae5e453/attachment-0001.html > > ------------------------------ > > Message: 6 > Date: Tue, 15 Nov 2011 10:32:16 -0300 (GMT-03:00) > From: "[email protected]" <[email protected]> > Subject: Re: [gmx-users] RMSD > To: <[email protected]> > Message-ID: > <10450993.2631321363936014.JavaMail.defaultUser@defaultHost> > Content-Type: text/plain; charset="iso-8859-1" > > > 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. > > > > regards > > > > Felipe > ----Mensaje original---- De: [email protected] Fecha: 15-nov-2011 > 10:18 Para: "Discussion list for GROMACS users"<[email protected]> > Asunto: Re: [gmx-users] RMSD On 11/15/11 8:23 PM, shahid nayeem wrote: > Dear all > 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. > Please help > shahid Nayeem > > > Try g_rmsf -res , it could be useful, maybe. > -- > Gianluca Santoni, > Institut de Biologie Structurale > 41 rue Horowitz > Grenoble > _________________________________________________________ > Please avoid sending me Word or PowerPoint attachments. > See http://www.gnu.org/philosophy/no-word-attachments.html > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/fb43cbe3/attachment-0001.html > > ------------------------------ > > Message: 7 > Date: Tue, 15 Nov 2011 19:48:06 +0530 > From: Harpreet Basra <[email protected]> > Subject: [gmx-users] Re: Positive potential energy for TFE solvent > To: [email protected] > Message-ID: > <caeaim5ssflvhhe+zm1z60t4b-bkuj5vcpbefza92g255qy2...@mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi Mark, > > Thanks for the quick reply. But i have already done what u suggested. > > > > > > On 15/11/2011 6:06 PM, Harpreet Basra wrote: > > > Hi > > > I am still stuck with same problem of obtaining positive potential > > > energy. > > > >>On 11/11/2011 5:07 PM, Harpreet Basra wrote: > > > >> Hi > > > >> > > > >> I am trying to generate an equilibrated box of 216 TFE molecules.To > > > >> generate the 216 TFE molecule box i performed following steps: > > > > > > > >A suggested workflow can be found here > > > >http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation > > > I have been following this link only. > > > > > > > > > > > >> 1) I got the tfe.gro file and created a cubic box of edge length = > > > >> 0.516 nm containing 1 TFE molecule (at its center), using the > > > >> following command: > > > >> > > > >>>> editconf -f tfe.gro -c -o tfe_box.gro -bt cubic -box 0.516 > > > >> I chose this length because in the tfe.gro file dimensions of the > TFE > > > >> molecule are 0.516 0.516 0.516. > > > > > > > >That's not a good reason. Choose a volume and shape that makes sense > for > > > >your target density. Cubic probably doesn't make sense when a > > > >rectangular shape is possible. Then you'll probably want to choose > -nbox > > > >differently later. > > > I chose a rectangular box too. still i get a positive value for PE and > > > moreover all the molecules move towards two opposite walls of the box. > > > I am not sure that the way I am using the genconf command is the > > > correct way. because I have tried every other possibility for not > > > getting a positive potential, with no success. So here are my .gro > > > file and the topology file for TFE. > > > *****tfe.gro file***** > > > 7 > > > > > > 1TFE F1T 1 0.444 0.344 0.246 > > > > > > 1TFE CT 2 0.334 0.245 0.246 > > > > > > 1TFE F2T 3 0.350 0.160 0.364 > > > > > > 1TFE F3T 4 0.350 0.160 0.127 > > > > > > 1TFE CH2T 5 0.187 0.326 0.246 > > > > > > 1TFE OT 6 0.075 0.220 0.246 > > > > > > 1TFE HT 7 -0.019 0.266 0.246 > > > > > > 0.49174 0.49174 0.49174 > > > > > > ****topology file**** > > > > > > [ moleculetype ] > > > > > > ; Name nrexcl > > > > > > TFE 3 > > > > > > [ atoms ] > > > > > > ; nr type resnr resid atom cgnr charge mass > > > > > > 1 FTFE 1 TFE F1T 1 -0.170 18.9984 > > > > > > 2 CTFE 1 TFE CT 1 0.452 12.0110 > > > > > > 3 FTFE 1 TFE F2T 1 -0.170 18.9984 > > > > > > 4 FTFE 1 TFE F3T 1 -0.170 18.9984 > > > > > > 5 CHTFE 1 TFE CH2T 1 0.273 14.0270 > > > > > > 6 OTFE 1 TFE OT 1 -0.625 15.9994 > > > > > > 7 H 1 TFE HT 1 0.410 1.0080 > > > > > > [ bonds ] > > > > > > ; ai aj fu c0, c1, ... > > > > > > 2 1 2 0.133 3380866.9 0.133 3380866.9 ; C1 F1 > > > > > > 2 3 2 0.133 3380866.9 0.133 3380866.9 ; C1 F2 > > > > > > 2 4 2 0.133 3380866.9 0.133 3380866.9 ; C1 F3 > > > > > > 2 5 2 0.153 7150000.0 0.153 7150000.0 ; C1 C2 > > > > > > 5 6 2 0.143 8180000.0 0.143 8180000.0 ; C2 O > > > > > > 6 7 2 0.100 15700000.0 0.100 15700000.0 ; O H > > > > > > [ pairs ] > > > > > > ; ai aj fu c0, c1, ... > > > > > > 1 6 1 ; F1 O > > > > > > 2 7 1 ; C1 H > > > > > > 3 6 1 ; F2 O > > > > > > 4 6 1 ; F3 O > > > > > > [ angles ] > > > > > > ; ai aj ak fu c0, c1, ... > > > > > > 1 2 3 2 109.5 520.0 109.5 520.0 ; F1 C1 F2 > > > > > > 1 2 4 2 109.5 520.0 109.5 520.0 ; F1 C1 F3 > > > > > > 1 2 5 2 109.5 520.0 109.5 520.0 ; F1 C1 C2 > > > > > > 3 2 4 2 109.5 520.0 109.5 520.0 ; F2 C1 F3 > > > > > > 3 2 5 2 109.5 520.0 109.5 520.0 ; F2 C1 C2 > > > > > > 4 2 5 2 109.5 520.0 109.5 520.0 ; F3 C1 C2 > > > > > > 2 5 6 2 109.5 520.0 109.5 520.0 ; C1 C2 O > > > > > > 5 6 7 2 109.5 450.0 109.5 450.0 ; C2 O H > > > > > > [ dihedrals ] > > > > > > ; ai aj ak al fu c0, c1, m, ... > > > > > > 6 5 2 1 1 0.0 5.9 3 0.0 5.9 3 ; dih O C2 C1 F1 > > > > > > 2 5 6 7 1 0.0 1.3 3 0.0 1.3 3 ; dih C1 C2 O H > > > > > > and to construct a box of TFE solvent i took the tfe.gro file and > > > replicated the TFE molecule by using > > > genconf -f tfe.gro -o tfe_sol.gro -rot -nbox 6 > > > can u plz suggest is it that I am using genconf in a wrong way that it > > > is causing this problem? I am not sure how many molecules (-nbox > > > option in genconf) should i keep in the box in order to get a mass > > > density of 1383g/L for TFE. > > > > That link says "Work out how much volume a single molecule would have in > > the box of your chosen density and size. Useeditconf > > <http://www.gromacs.org/editconf>to place a box of that size around your > > single molecule." It does not seem to me that you have done this. > > > > Mark > > > > I did place the *single molecule* in a box of size required to get a > density of 1383 g/L. I also checked the density of the solvent box > (containing 216 molecules after NVT equilibration for 200 ps) I constructed > the average value comes out to be 1397 g/L with a std deviation of 30 g/L, > thus it seems range. Moreover, the potential energy of this one molecule > (tfe.gro) was coming out to be highly negative (-6.4E+08 kJ/mol). But on > generating a solvent system with 216 TFE molecules the energy becomes > (1.9E+04 kJ/mol). > > Harpreet > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111115/87c00073/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 91, Issue 104 > ****************************************** > -- Arun Kumar Somavarapu Project-JRF Dr. Prasanna's lab TMC, ACTREC Navi Mumbai-410210
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