Re: [gmx-users] unexpecter rmsd
Thank you Justin On Fri, Mar 27, 2020, 19:47 Justin Lemkul wrote: > > > On 3/27/20 11:10 AM, Emran Heshmati wrote: > > Thanks to Paul and jorden, I repost my question: > > I am working on a protein consisting 2 chains. After performing > > regular MD simulation > > and analysis the outputs, I got unexpecter rmsd, as seen in link below. > > What is the problem?? > > https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html > > This is a PBC effect, with one or more protein chains jumping across a > periodic boundary. Recenter with trjconv. You may have to center on one > of the chains individually to get proper wrapping of the unit cell. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 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. > -- 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.
[gmx-users] unexpecter rmsd
Thanks to Paul and jorden, I repost my question: I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as seen in link below. What is the problem?? https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.html -- 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.
[gmx-users] Inexpected rmsd
I am working on a protein consisting 2 chains. After performing regular MD simulation and analysis the outputs, I got unexpecter rmsd, as shown in arttached graph. What is the problem? -- 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.
[gmx-users] gmx distance
Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall dist.xvg -oh disthist.xvg -b 7 -e 10 but don't list r130 and r153 as extra groups. Adding -n *.ndx option didn't sole the problem. Any comment please. -- 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.
[gmx-users] (no subject)
Dear All I am in trouble with gmx distance command. I want to calculate the distance between two amino acids (residue 130 and residue 153) in a protein after gromacs standard simulation. After generating of r130.ndx and r153.ndx index files, I use this command: gmx distance -f md_0_1_noPBC.xtc -s md_0_1.tpr -oav distave.xvg -oall dist.xvg -oh disthist.xvg -b 7 -e 10 but don't list r130 and r153 as extra groups. Adding -n *.ndx option didn't sole the problem. Any comment please. -- 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.
[gmx-users] Protein dipole moments
What are the physical meaning of <|M|^2> and <|M|>^2 in the outputs of gmx dipoles command ?? Any help is welcome. -- 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.
Re: [gmx-users] residue number in secondary structure plot
Than you Justin. I used CHARMM force field. On Sat, Sep 9, 2017 at 10:38 PM, Justin Lemkul wrote: > > > On 9/9/17 1:58 PM, Emran Heshmati wrote: > >> Dear Gromacs users >> I performed a md simulation on apeptide fragment consist of 16 aa . when I >> analysed its secondary structure content using "gmx do_dssp " command, >> there was only 15 aa in y-axis in resultig *.eps file format. can anyone >> explain this controversy. >> > What force field did you use? IIRC, the code doesn't recognize CHARMM > C-terminal oxygen atoms correctly so the program ignores them. > > -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.biochem.vt.edu/people/faculty/JustinLemkul.html > > == > > -- > 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. -- 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.
[gmx-users] residue number in secondary structure plot
Dear Gromacs users I performed a md simulation on apeptide fragment consist of 16 aa . when I analysed its secondary structure content using "gmx do_dssp " command, there was only 15 aa in y-axis in resultig *.eps file format. can anyone explain this controversy. -- 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.
Re: [gmx-users] difference in potential energy
Thanks to mark for his explanations. We performed MD simulation on a peptide fragment as well as its mutants where, its residues have been systematically replaced by alanine residue. We found that potential and kinetic energies of one mutant (T=>A) is significantly different from other molecules. interestingly there are other similar substitutions in different positions indicating that molecules with similar masses and chemical formula are being compared. apparently, we are facing with an special case in which the changing of the position of a residue has profound effect on the kinetic and potential energies. our question is related to the interpretation of this finding!! Regards Emran On Sun, Jun 25, 2017 at 2:45 AM, Emran Heshmati wrote: > Dear Gromacs users > I performed alanine scaning mutagenesis using gromacs on a peptide > fragment consisting 16 aa. In one of the mutations, the kinetic energy of > the system was significantly different. How can I interpret this result? > any comment is welcome > regards > Emran > -- 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.
[gmx-users] difference in kinetic energy
Dear Gromacs users I performed alanine scaning mutagenesis using gromacs on a peptide fragment consisting 16 aa. In one of the mutations, the kinetic energy of the system was significantly different. How can I interpret this result? any comment is welcome regards -- 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.
[gmx-users] difference in potential energy
Dear Gromacs users I performed alanine scaning mutagenesis using gromacs on a peptide fragment consisting 16 aa. In one of the mutations, the kinetic energy of the system was significantly different. How can I interpret this result? any comment is welcome regards Emran -- 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.
[gmx-users] positive potential energy
Hi all I run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? -- 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.
Re: [gmx-users] (no subject)
total charge of your molecule depends on ionizable groups on your molecule and the pH. Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: Shivangi Agarwal To: gmx-us...@gromacs.org Sent: Friday, 16 June 2017, 18:24 Subject: Re: [gmx-users] (no subject) Ya sir But for ATB, it is asking for total charge. How to calculate total charge? On 16 Jun 2017 18:59, "Justin Lemkul" wrote: > > > On 6/16/17 8:03 AM, Shivangi Agarwal wrote: > >> Hi all >> >> When i am generating a ligand topology using PRODRG, I am getting topology >> file with hydrogens deleted in it. Which another server can I use for >> ligand topology generation? >> >> > GROMOS is a united-atom force field, so the aliphatic H atoms are not > going to be explicitly represented; you should check your assumptions about > force fields and which one you should be using if this comes as a surprise > :) PRODRG is not of sufficient quality for MD simulations without > significant manual revision. ATB is better if you want to use a GROMOS > parameter set. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > 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. > -- 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. -- 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.
Re: [gmx-users] (no subject)
Find these addresses:1- LigParGen Server | | | LigParGen Server | | | 2- SwissParam - Topology and parameters for small organic molecules | | | SwissParam - Topology and parameters for small organic molecules Determine topology and parameters for small organic molecules, for use with CHARMM or GROMACS | | | 3- https://atb.uq.edu.au/ Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: Shivangi Agarwal To: gmx-us...@gromacs.org Sent: Friday, 16 June 2017, 16:34 Subject: [gmx-users] (no subject) Hi all When i am generating a ligand topology using PRODRG, I am getting topology file with hydrogens deleted in it. Which another server can I use for ligand topology generation? Regards -- 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. -- 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.
Re: [gmx-users] Vmd error
Dear Rahulyou can visualize your final *.xtc output in another tool/software first, to ensure your simulation steps. Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to From: RAHUL SURESH To: "gmx-us...@gromacs.org" Sent: Friday, 16 June 2017, 9:04 Subject: [gmx-users] Vmd error I extended my simulation of a free protein from 100ns to 150ns. Corresponding files are extend.gro and extend.xtc. I applied pbc conditions and my new xtc s newmd.xtc. I tried to visualise my trajectory in vmd I uploaded the extend.gro file and loaded newmd.xtc in gro file. But I couldn't visualise the trajectory. No frames are read. Am doing anythg wrong? Thank you so much for your valuable advice. -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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. -- 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.
[gmx-users] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
[gmx-users] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
[gmx-users] Positive potential energy
Hi allI run two simulations on a 16 aa peptide under the same conditions (forcefield, simulation duration, ...) except the solvent in one of the simulations was TFE instead of water. The potential energy in the TFE containing system was positive (about 14 Kj/mol), while in water containing system was negative (about -7 Kj/mol). Is it normal? or some kind of error has occurred? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
[gmx-users] nano structure simulation
Dear Gromacs usersI want to simulate the effects of a nano structure (such as graphene oxide) on the structure of a protein but I have problems in constructing nano structure topology file. Do anyone have an explained tutorial? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
[gmx-users] TFE
Dear Gromacsians I want to simulate a protein (MAJOR PRION PROTEIN) structure in TFE (trifluoroethanol) instead of water. I followed these steps: 1- I build tfe.pdb and tfe.itp using ATb server, (gromos force field: G54A7FF) 2- I placed tfe.itp file in directories: /usr/share/gromacs/top and /usr/share/gromacs/top/gromos54a7.ff 3- I build tfe.gro from tfe.pdb using editconf command (editconf -f tfe.pdb -o tfe.gro) and placed it in the working directory. 4- I followed jastin lemkul recommended procedure ((lysozyme in water)): pdb2gmx -f 4HE7.pdb -o 4HE7_processed.gro editconf -f 4HE7_processed.gro -o 4HE7_newbox.gro -c -d 0.75 -bt dodecahedron genbox -cp 4HE7_newbox.gro -cs tfe.gro -o 4HE7_solv.gro -p topol.top but the latest step (genbox command) takes too long and remains unfinished. this is what I see in the terminal: Reading solute configurationMAJOR PRION PROTEINContaining 159 atoms in 16 residuesInitialising van der waals distances... WARNING: Masses and atomic (Van der Waals) radii will be guessedbased on residue and atom names, since they could not bedefinitively assigned from the information in your inputfiles. These guessed numbers might deviate from the massand radius of the atom type. Please check the outputfiles if necessary. Reading solvent configuration"ALL ATOM STRUCTURE FOR MOLECULE UNK"solvent configuration contains 9 atoms in 1 residues what is wrong? help me please. Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
[gmx-users] Charge of the system
Dear allI am using gromacsto simulate ligand bonding to an enzyme. I have two problems withcharge of system: 1) after making topology file for ligand using prodrug, I saw itsnet charge was -0.4. how can I neutralize it?2) I used this topology parameters of ligand to continuesimulation steps. After adding these parameters to protein topologyfile (as proposed by Lemkul) , the net charge of the system waschanged from 0 to -4. Is it needed to neutralize the system again oranything els? Best Regards Emran Heshmati Ph. D.Biophysicist,Computational Bio-Chemist P Save a tree... please don't print this e-mail unless you really need to -- 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.
