Dear Justin Thanks for your reply
Yes I edited the topology and resolved the problem Best Farial On Tue, Nov 13, 2018 at 3:34 AM < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@maillist.sys.kth.se > > To subscribe or unsubscribe via the World Wide Web, visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or, via email, send a message with subject or body 'help' to > gromacs.org_gmx-users-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@maillist.sys.kth.se > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gromacs.org_gmx-users digest..." > > > Today's Topics: > > 1. Re: Expansion system after NVT Equilibrium in Gromacs > (Justin Lemkul) > 2. Re: Input file for energy minimization for solvated system: > Error (Justin Lemkul) > 3. Re: pdb2gmx fatal error (Ali Khodayari) > 4. Re: Group WAT referenced in the .mdp file was not found in > the index file (Justin Lemkul) > 5. Re: atomtype OV not found (Justin Lemkul) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Nov 2018 18:59:01 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Expansion system after NVT Equilibrium in > Gromacs > Message-ID: <f2bfba5b-cc1a-329b-de4b-5b264d4e4...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 11/11/18 12:16 PM, yasmineso...@students.itb.ac.id wrote: > > i'm currently running a simulation protein in water using gromacs with > force field gromos96 54a7. the protein structure that i used is from > modeller. there is no problem untill the minimization step but the system > is expanding after NVT equilibration. and when i try to do NPT > equilibration after that, the system is shrinking [the box volume is > smaller than before] > > > > i'm using the parameter from gromacs tutorial "lysozyme in water" with > hbonds constraints for NVT equilibration and the temperature is 298 K. > please help me to solve this problem > > Don't use input files from my tutorial if you're using GROMOS. The > nonbonded settings and required constraints are different, as hopefully > I make very clear... > > In any case, if you're running NPT, naturally the system will expand and > contract. There's no reason that it won't, as that is precisely what a > barostat does. If your system is changing, that just means your initial > conditions are not compatible with the specified NPT ensemble and the > properties of the system have to adjust. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 2 > Date: Mon, 12 Nov 2018 19:00:23 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Input file for energy minimization for > solvated system: Error > Message-ID: <ab0c1a33-c48d-9cdc-c4db-110582198...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 11/11/18 3:04 PM, Neena Susan Eappen wrote: > > Hello GROMACS users, > > > > > > I was trying to create an input file for energy minimization of solvated > system, using the following command: > > > > grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o > protein-EM-solvated.tpr > > > > Got the following error: > > number of coordinates in coordinate file (1y6l-solvated.gro, 181577) > does not match topology (1y6l.top, 182265). > > > > I think the following error occurred because I skipped the following > step: > > Edit the topology file and decrease the number of solvent molecules. > Also add a line specifying the number of NA ions and a line specifying the > amount of CL. > > > > My question: > > > > 1. How to open the topology file? > > A topology is a plain text file. Use a plain-text editor. > > > 2. How do I determine number of NA and CL ions added? I just saw a > massive list of these counterions being added, but not the total number. > > genion tells you this. > > > 3. My net charge on the protein was 6+, why do I need to add Na+ > ions? > > We don't know what your genion command was, so we can't say. > > Let solvate and genion do the work for you. Use the -p flag to have > those programs update your topology for you, especially if you are not > familiar with their contents or how to edit them. See e.g. > http://www.mdtutorials.com/gmx/lysozyme/index.html > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 3 > Date: Tue, 13 Nov 2018 00:01:24 +0000 > From: Ali Khodayari <ali.khoday...@student.kuleuven.be> > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] pdb2gmx fatal error > Message-ID: <d295cef0-7278-4486-93f3-0d3847350...@student.kuleuven.be> > Content-Type: text/plain; charset="us-ascii" > > Dear Justin, > > Thank you for your full explanation. That made it all clear now. > > Kind regards, > Ali > > > On 13 Nov 2018, at 00:57, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > On 11/8/18 1:37 PM, Ali Khodayari wrote: > >> Dear Justin, > >> > >> Thank you for your response. Yet, I have not been able to solve the > problem. > >> > >> The structure looks fine but gromacs is complaining about a dangling > atom at > >> one of the terminal ends, if I choose no terminal to be added. While, > > > > You can't "see" a dangling bond by visualizing the structure. That term > refers exclusively to an incomplete terminus in terms of the *topology* > that is being generated for the system. Maybe atoms are missing or an > inappropriate terminal patch is being applied; either would generate that > error. But again I emphasize the fact that a chain of glucose has first and > last residues that are structurally and topologically different from > internal, linked monomers. It's basic chemistry. > > > > <snip> > > > >> ATOM 27 O3 GLC0 2 3.909 5.661 5.002 1.00 0.04 > >> O > >> ATOM 28 HO4 GLC0 2 4.850 3.729 10.263 1.00 0.00 > >> H > >> ATOM 29 O1 GLC0 1 3.396 2.685 4.467 1.00 0.04 > >> O > > > > Here's your problem - your residue numbers alternate back and forth > between 1 and 2. pdb2gmx ignores these and uses its own numbering, > incrementing the internal counter whenever the residue number changes. So > to pdb2gmx, your input file is full of incomplete residues. > > > >> ATOM 30 O5 GLC0 2 4.225 2.770 8.173 1.00 0.04 > >> O > >> ATOM 31 O6 GLC0 2 3.558 0.309 5.328 1.00 0.04 > >> O > >> ATOM 32 H1 GLC0 2 2.572 4.115 8.609 1.00 0.00 > >> H > >> ATOM 33 H2 GLC0 2 5.244 5.151 7.307 1.00 0.00 > >> H > >> ATOM 34 H3 GLC0 2 2.361 4.651 6.153 1.00 0.00 > >> H > >> ATOM 35 H4 GLC0 2 5.141 3.258 5.636 1.00 0.00 > >> H > >> ATOM 36 H5 GLC0 2 2.480 2.262 6.979 1.00 0.00 > >> H > >> ATOM 37 H61 GLC0 2 3.879 0.196 7.468 1.00 0.00 > >> H > >> ATOM 38 H62 GLC0 2 5.286 0.920 6.494 1.00 0.00 > >> H > >> ATOM 39 HO2 GLC0 2 2.496 6.480 7.836 1.00 0.00 > >> H > >> ATOM 40 HO3 GLC0 2 5.015 5.674 4.919 1.00 0.00 > >> H > >> ATOM 41 HO6 GLC0 2 2.453 0.270 5.418 1.00 0.00 > >> H > >> ATOM 42 O3 GLC0 1 3.852 1.653 -0.348 1.00 0.00 > >> O > > > > As above, now you're again going back and forth between 1 and 2, so > pdb2gmx sees a new residue, which is not correct. > > > > -Justin > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > > > ------------------------------ > > Message: 4 > Date: Mon, 12 Nov 2018 19:01:29 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Group WAT referenced in the .mdp file was not > found in the index file > Message-ID: <b6d71208-268a-dbc6-0a7b-3c015dec1...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 11/12/18 7:14 AM, Rahma Dahmani wrote: > > Hi GMX users, > > > > i double checked in my topology and gro files that i am using the same > > moleculetype ( LIG and WAT) but when i run grompp for T equilibration i > get > > an error message """" Group WAT referenced in the .mdp file was not found > > in the index file """" > > PS: i am not using an index file and i modified tc-grps, in nvt.mdp > file , > > to : > > tc-grps = LIG WAT . > > > > The error means that "WAT" is not a valid group. What is it in your > topology? The default water [moleculetype] in all GROMACS top > <https://maps.google.com/?q=t+water+%5Bmoleculetype%5D+in+all+GROMACS+top&entry=gmail&source=g>ologies > is > "SOL," not "WAT." > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > Message: 5 > Date: Mon, 12 Nov 2018 19:02:52 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] atomtype OV not found > Message-ID: <10e914b3-e342-78e3-141e-7a541cc18...@vt.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 11/12/18 8:41 AM, Farial Tavakoli wrote: > > Dear Mark > > > > I changed the way of topology generating in AMBER. The peptidic ligand > (has > > 2 phosphotyrosine residues) topology was generated using amber. all of > the > > files that I have in my working directory are, Leaprc.ff99SB, > > Learc.phosaa10, frcmod.phosaa10, ligand.inpcrd, ligand.prmtop. The > only > > thing that I know to convert amber format to gromacs format is to use > > acpype python script : > > python acpype -p ligand.prmtop -x ligand.inpcrd > > The .gro and .top files were generated. protein topology was generated > > using amber99SB ff in gromacs and then complex.gro and .top files were > > modified according to the tutorial in gromacs. But now, when I issue this > > command: > > gmx grompp -f .mdp -c .gro -p .top -o ions.tpr > > I face to this error: > > ERROR 1 [file mig_GMX.itp, line 60]: > > Atomtype OV not found > > OV atom is related to leaprc.phosaa10 file and I dont know what should I > do > > now? > > I think , the leaprc.phosaa10 file has to be added to aminoacid.rtp file > of > > amber99SB.ff but I dont know how to convert it to gromacs format file? > > Am I right? > > WOuld you please guide me how to remove this Error? > > Your force field has to account for all the atom types required to run > the simulation. You don't need to modify any .rtp files if you've > already got a topology produced by other means. But that topology should > be edited to introduce any new atom types required, associated bonded > parameters, etc. When you do nonstandard things, you have to take > nonstandard approaches... > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 175, Issue 40 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.