Dr Justin This is my Topolofy file for Ethanol [ moleculetype ] ; Name nrexcl Protein 3
[ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 H 1 ETHH EH 1 0.408 1.008 ; qtot 0.408 2 OA 1 ETHH EO 1 -0.674 15.9994 ; qtot -0.266 3 CH2 1 ETHH EC1 1 0.266 14.027 ; qtot 0 4 CH3 1 ETHH EC2 2 0 15.035 ; qtot 0 [ bonds ] ; ai aj funct c0 c1 c2 c3 1 2 2 gb_1 2 3 2 gb_18 3 4 2 gb_27 [ pairs ] ; ai aj funct c0 c1 c2 c3 1 4 1 [ angles ] ; ai aj ak funct c0 c1 c2 c3 1 2 3 2 ga_12 2 3 4 2 ga_15 [ dihedrals ] ; ai aj ak al funct c0 c1 c2 c3 c4 c5 1 2 3 4 1 gd_23 ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include ethanol topology #include "ethanol.itp" ; Include water topology #include "spc.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name GROwing Monsters And Cloning Shrimps in water [ molecules ] ; Compound #mols Protein 1 ETHH 1852 SOL 4000 On Tue, 18 Sep 2012 15:00:07 +0200 (CEST), gmx-users-request wrote > Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > 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 > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > Today's Topics: > > 1. Hbond-ETH-WATER (Praveen Kumar Sappidi) > 2. Re: charge calculation........ (tarak karmakar) > 3. why traj.trr appears (Dr. Vitaly Chaban) > 4. Re: Hbond-ETH-WATER (Justin Lemkul) > 5. Re: why traj.trr appears (Justin Lemkul) > 6. Re: LINCS warning in md run > (reising...@rostlab.informatik.tu-muenchen.de) > 7. Re: Hbond-ETH-WATER (Justin Lemkul) > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 18 Sep 2012 18:38:41 +0630 > From: "Praveen Kumar Sappidi" <ch11d...@smail.iitm.ac.in> > Subject: [gmx-users] Hbond-ETH-WATER > To: gmx-users@gromacs.org > Message-ID: <20120918120320.m14...@smail.iitm.ac.in> > Content-Type: text/plain; charset=utf-8 > > Hi all > Am Simulating Ethanol-water system using Gromacs4.0.7 > the problem is am not able to calculate number of hydrogen bonds in > ethanol and water-ethanol. i can see a small peak at 0.24 of Ethanol- > water RDFs and visually also i can see hydrogen bonding is formed > > am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg > > please help if anyone knows the solution > -- > Thanks & Regards > Praveenkumar Sappidi > Research Scholar > Molecular modelling and simulation lab > Chemical Engineering Department > IIT Madras-600036 > Chennai,INDIA > > ------------------------------ > > Message: 2 > Date: Tue, 18 Sep 2012 17:41:31 +0530 > From: tarak karmakar <tarak20...@gmail.com> > Subject: Re: [gmx-users] charge calculation........ > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: > <cagzmootw6jkd6rzgbodkjebzym67d9ejgaprjhnru8n27yz...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Thanks Mark. > > I have gone through the link "Parameterization of novel molecules" > and I see quantum calculations can be handy for this type of charge > calculation (AMBER). So for the unprotonated tyrosine, I am taking > two more amino acids (left and right) and calculating ESP charges of > the tri-peptide by using HF / 6-31(+)g(d) level of theory. Can you please > tell me whether I can include the partial charges of all the atoms of > the middle tyrosine (unprotonated) in the aminoacids.rtp file to > simulate the protein ? > > Thanks, > Tarak > > On Mon, Sep 17, 2012 at 6:21 PM, Mark Abraham > <mark.abra...@anu.edu.au> wrote: > > On 17/09/2012 10:01 PM, tarak karmakar wrote: > >> > >> Dear All, > >> > >> I want to have one of tyrosine residues in my protein to > >> be unprotonated. I am using amber force field for the simulation. But > >> in aminoacid.rtp there is no entry for the unprotonated one. So I am > >> adding it by myself in to the .rtp file. Now I am bit confused with > >> the charge of the unprotonated one. How can I calculate the partial > >> charges for each and every atoms in unprotonated tyrosine? Would > >> Gaussian/SCF be a good one to deal with this matter? Should I take the > >> tyrosine amino acid alone to calculate the charge in Gaussian ? > >> Please suggest me the proper method(s) to calculate the charge. > > > > > > It varies, but should be determined by the process by which the rest of the > > force field was determined. See > > http://www.gromacs.org/Documentation/How-tos/Parameterization > > > > Mark > > -- > > gmx-users mailing list gmx-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 > > ------------------------------ > > Message: 3 > Date: Tue, 18 Sep 2012 14:29:23 +0200 > From: "Dr. Vitaly Chaban" <vvcha...@gmail.com> > Subject: [gmx-users] why traj.trr appears > To: gmx-users@gromacs.org > Message-ID: > <CAPXdD+bmndF0Mt-ssf7Nq9C5C-BOz+ipibZvErUZT=2qotf...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Dear All - > > I an using the current version of gromacs. Although I have > > nstxout = 0 > nstvout = 0 > nstfout = 0 > > in the MDP file, the traj.trr file appears during the MD run (and is > quite large). In older versions, there was no traj.trr with such an > input. > > Did I miss something, please? > > Dr. Vitaly V. Chaban, 430 Hutchison Hall > Dept. Chemistry, University of Rochester > 120 Trustee Road, Rochester, NY 14627-0216 > THE UNITED STATES OF AMERICA > > ------------------------------ > > Message: 4 > Date: Tue, 18 Sep 2012 08:28:17 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Hbond-ETH-WATER > To: ch11d...@smail.iitm.ac.in, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: <505868e1.4050...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 9/18/12 8:08 AM, Praveen Kumar Sappidi wrote: > > Hi all > > Am Simulating Ethanol-water system using Gromacs4.0.7 > > the problem is am not able to calculate number of hydrogen bonds in > > ethanol > > and water-ethanol. > > i can see a small peak at 0.24 of Ethanol-water RDFs and visually also i > > can > > see hydrogen bonding is formed > > > > am using command g_hbond -f *.xtc -s *.tpr -n *.ndx -num .xvg > > > > please help if anyone knows the solution > > You haven't described why the above command failed to produce what > you wanted. g_hbond should prompt you to choose groups, which should > include ethanol and water, so you can create plots of ethanol- > ethanol, water-water, and ethanol-water hydrogen bonds. > > -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 > > ======================================== > > ------------------------------ > > Message: 5 > Date: Tue, 18 Sep 2012 08:43:16 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] why traj.trr appears > To: vvcha...@gmail.com, Discussion list for GROMACS users > <gmx-users@gromacs.org> > Message-ID: <50586c64.8020...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 9/18/12 8:29 AM, Dr. Vitaly Chaban wrote: > > Dear All - > > > > I an using the current version of gromacs. Although I have > > > > nstxout = 0 > > nstvout = 0 > > nstfout = 0 > > > > in the MDP file, the traj.trr file appears during the MD run (and is > > quite large). In older versions, there was no traj.trr with such an > > input. > > > > Did I miss something, please? > > > > The above combination should turn off production of a .trr file. > Something doesn't add up. Verify your settings in the .log and/or > .tpr file - perhaps you've mixed up .mdp files. > > -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 > > ======================================== > > ------------------------------ > > Message: 6 > Date: Tue, 18 Sep 2012 14:58:41 +0200 > From: reising...@rostlab.informatik.tu-muenchen.de > Subject: Re: [gmx-users] LINCS warning in md run > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Message-ID: <f2e9b5cfb5297c858d42968f1871b0bd.squir...@rostlab.org> > Content-Type: text/plain;charset=iso-8859-1 > > Okey, > now I tried it without any fixed residues. But still the energy > after the minimization is not very low and I still get the LINCS warnings. > > The mdp file I use for the minimization looks like this: > > define = -DPOSRES > integrator = steep > emtol = 10 > nsteps = 1500 > nstenergy = 1 > energygrps = System > coulombtype = PME > rcoulomb = 0.9 > rvdw = 0.9 > rlist = 0.9 > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-5 > pbc = xyz > > the mdp file for the md run looks like this: > > define = -DPOSRES > integrator = md > dt = 0.001 > nsteps = 5000 > nstxout = 100 > nstvout = 0 > nstfout = 0 > nstlog = 1000 > nstxtcout = 500 > nstenergy = 5 > energygrps = Protein Non-Protein > nstcalcenergy = 5 > nstlist = 10 > ns-type = Grid > pbc = xyz > rlist = 0.9 > coulombtype = PME > rcoulomb = 0.9 > rvdw = 0.9 > fourierspacing = 0.12 > pme_order = 4 > ewald_rtol = 1e-5 > gen_vel = yes > gen_temp = 200.0 > gen_seed = 9999 > constraints = all-bonds > tcoupl = V-rescale > tc-grps = Protein Non-Protein > tau_t = 0.1 0.1 > ref_t = 298 298 > pcoupl = no > > The output of the minimization run is: > > Steepest Descents converged to machine precision in 15 steps, > but did not reach the requested Fmax < 10. > Potential Energy = -7.9280412e+05 > Maximum force = 1.0772942e+04 on atom 979 > Norm of force = 9.6685356e+01 > > The output of the MD run is: > > Step 1031, time 1.031 (ps) LINCS WARNING > relative constraint deviation after LINCS: > rms 0.001431, max 0.010707 (between atoms 976 and 979) > bonds that rotated more than 30 degrees: > atom 1 atom 2 angle previous, current, constraint length > 976 979 81.6 0.1272 0.0970 0.0960 > > The atom 979 is the hydrogen atom on the phosphate. There has to be one > hydrogen atoms because it is protonated once. The other atom 976 is the > oxygen atom where the hydrogen atom is bound to. > The bounding parameters for this kind of binding were already there. > I didn't add them. > > I already did it for another phosphorylation on another position in this > structure. And here I also got many LINCS errors. And again the > problem is the connection between the hydrogen atom and the oxygen atom. > > But I do not understand why. > Can you please help me?! > > > > > > On 9/18/12 7:22 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: > >> I need the rest of the structure just as it is now because I want to do > >> electrostatic analysis with it. > > > > Another thing worth considering - why do you necessarily need the rest of > > the > > structure to be identical? Or perhaps better stated, why do you believe > > this to > > be the more appropriate model of reality? Phosphorylation events > > frequently > > trigger structural changes in the protein, so I see no reason to assume it > > will > > have no effect on the rest of the structure. At the very least, you can > > try a > > "normal" EM and MD procedure without freezing anything to see if you can > > determine the problem. If things run normally without freezing, then you > > know > > that whatever you are doing here is artificial and problematic. > > > > -Justin > > > >> I just added the phosphate manually and so I want to minimize and run a > >> short MD with it. > >> > >> I added the dihedraltype of the amber database > >> (http://personalpages.manchester.ac.uk/staff/Richard.Bryce/amber/pro/frcmod_y1p) > >> to the ffbonded file. > >> And additionally I looked at the protein and made all the residues which > >> could somehow influence the protein flexible so that eventual clashes > >> can > >> be repaired. > >> But still I got the error: > >> > >> ..Step 3612, time 3.612 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 0.000008, max 0.000031 (between atoms 975 and 978) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 976 979 32.6 0.0961 0.0960 0.0960 > >> > >> Step 3613, time 3.613 (ps) LINCS WARNING > >> relative constraint deviation after LINCS: > >> rms 0.000237, max 0.001400 (between atoms 976 and 979) > >> bonds that rotated more than 30 degrees: > >> atom 1 atom 2 angle previous, current, constraint length > >> 976 979 33.4 0.0960 0.0959 0.0960 > >> .. > >> > >> Too many LINCS warnings (1000) > >> > >> > >> I already minimized the protein and everything was fine. There were no > >> errors: > >> > >> Steepest Descents converged to machine precision in 15 steps, > >> but did not reach the requested Fmax < 10. > >> Potential Energy = -7.7436938e+05 > >> Maximum force = 8.6871973e+03 on atom 979 > >> Norm of force = 7.1224258e+01 > >> > >> gcq#49: "You Could Make More Money As a Butcher" (F. Zappa) > >> > >> > >> Steepest Descents converged to machine precision in 15 steps, > >> but did not reach the requested Fmax < 10. > >> Potential Energy = -7.7436938e+05 > >> Maximum force = 8.6871973e+03 on atom 979 > >> Norm of force = 7.1224258e+01 > >> > >> > >> And also during the grompp run there are no errors. > >> Can you please help me to find out where the problem lies? > >> > >> > >> Thank you, > >> Eva > >> > >> > >>> > >>> > >>> On 9/13/12 5:50 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: > >>>> Ah okey. Thank you. > >>>> I will write them. > >>>> > >>>> Hmm, but the protein is a crystal structure from pdb with a resolution > >>>> of > >>>> 1.2. I already added the hydrogen atoms to this structure and there I > >>>> already minimized them and made a md run. And there were no errors. > >>>> And > >>>> now I only added the phosphate to the minimized structure. So I > >>>> thought > >>>> that I only had to minimize the phosphate and the residue it bound on. > >>>> Or is there a mistake in my thought here? > >>> > >>> If adding the phosphate resulted in a crash, then clearly that's the > >>> problem. I > >>> don't understand why you would run EM on just the phosphate and keep > >>> the > >>> rest of > >>> the protein structure frozen. Again, that potentially prevents clashes > >>> from > >>> being resolved. I don't understand what value there is in only > >>> minimizing > >>> the > >>> phosphate. > >>> > >>> -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@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 > >>> > >> > >> > > > > -- > > ======================================== > > > > 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@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 > > > > ------------------------------ > > Message: 7 > Date: Tue, 18 Sep 2012 08:58:08 -0400 > From: Justin Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Hbond-ETH-WATER > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <50586fe0.5010...@vt.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > On 9/18/12 8:56 AM, Praveen Kumar Sappidi wrote: > > Hi Justin > > prompt for calculation i have shown below > > > > Reading file eth-water60%-production.tpr, VERSION 4.0.7 (single precision) > > Note: tpx file_version 58, software version 73 > > Specify 2 groups to analyze: > > Group 0 ( System) has 19412 elements > > Group 1 ( ETHH) has 7412 elements > > Group 2 ( SOL) has 12000 elements > > Group 3 ( EC1) has 1853 elements > > Group 4 ( EC2) has 1853 elements > > Group 5 ( EO) has 1853 elements > > Group 6 ( OW) has 4000 elements > > Group 7 ( EH) has 1853 elements > > Group 8 ( HW1) has 4000 elements > > Group 9 ( HW2) has 4000 elements > > Select a group: 1 > > Selected 1: 'ETHH' > > Select a group: 2 > > Selected 2: 'SOL' > > Checking for overlap in atoms between ETHH and SOL > > Calculating hydrogen bonds between ETHH (7412 atoms) and SOL (12000 atoms) > > Found 4000 donors and 4000 acceptors > > Reading frame 0 time 0.000 > > Will do grid-seach on 15x15x15 grid, rcut=0.35 > > Reading frame 2000 time 4000.000 > > Average number of hbonds per timeframe 0.000 out of 8e+06 possible > > > > Can you please post your topology for ethanol? I suspect your atoms > are named in a way that g_hbond doesn't not recognize, since the > number of donors and acceptors seem to only correspond to water > (12000/3 = 4000). > > -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@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! > > End of gmx-users Digest, Vol 101, Issue 52 > ****************************************** -- Thanks & Regards Praveenkumar Sappidi Research Scholar Molecular modelling and simulation lab Chemical Engineering Department IIT Madras-600036 Chennai,INDIA -- gmx-users mailing list gmx-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