[gmx-users] topology servers versus ff.
Dear gromacs users.. while using charmm27 can i use PRODRUG for topology building.?? when im using prodrug pdb2gmx gives me error of missing atoms but when i use charmm ff,it doesnt give me that error,so proceeding with charmm27 i made ligand topology by prodrug and used it for further simulation,when comes to adding ions step it gives me error of ""atomtypes CH3 not found"". thanks. -- 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] DNA topology error
dear Mark Abraham According to my error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.""" if O5' can be set in pdb manually,then how the other values of cordinates (figures) can be provided manually,as these values are experimental. Thanks. Maria. -- 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] DNa topology error.
Thanks Mark Abraham. i would like to share my pdb file as still i dont understand the error as well as your answer,kindly look at this then explain it. it cant be shared as the file is large.i checked the file in front of residue 9,there is no DG at all .All along the chains is DA. 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] Error of DNA topology
Dear gromacs user. i am simulating protein having DNA ,,when i applied for pdb to gmx command,it gives me error like """Residue 9 named DG of a molecule in the input file was mapped to an entry in the topology database, but the atom O5' used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed.""" while using charmm27 all-atom ff.By using gromos 96 43a1 ff, it doesnt form topology for DNA kindly give me a detail answer. thanks -- 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] Parameterization for noval molecules.
Dear Gromacs users. Can anybody who are good in parameterization, make parameters for the molecule of my interest..As i am a beginner and was told on this forum that parameterization is not for beginners. Thanks.. -- 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 Erik.. I have studied the manuals of gromacs and from that i came to know that gromacs use united atom ff thats why i asked and in manuals many things has been explained by quantum basis,,which is not understandable for me. How can i find ff parameters for my ligand of interest?? also if ff parameters are not in published form then it means i will not be able to use that ligand for MD run?? My ligand of interest is alkaloid. and i dont know how can i make the parameters for it. Thank you. -- 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] Charmm ff compatibility with Gromacs
Hello Gromacs users.. Charmm 37 ff is for charmm and Namd which is all atom ff using codes,,and gromacs is united atom so how can its results will be reliable as these are different things??.My protein of interest is having DNA.. Secondly how can i find ff parameters for my ligand of interest?? also if ff parameters are not in published form then it means i will not be able to use that ligand for MD run?? 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] ignoring -h atoms
Dear ERIK.. """..No. -ignh ignores the hydrogen atoms in the input structure, but uses the rtp file(s) to generate new hydrogens. This is useful, for example, when some hydrogens are missing in the pdb file. The structure and topology will therefore contain hydrogens in the end also with -ignh.""".. now i have confusion if the ff ist ignore it and then in rtp files consider it..so why it at ist it ignores..there is no need to do so.after all h-atom will be same if it is in input file or when later form by rtp file. secondly what will be the consequences,,if in case it is ignored or not ignored..would it make difference to results in both cases.and if there would difference in results,,what kind of results are more reliable.??? 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] Ignoring H-atoms.
Dear Gromacs users,, if igoring h-atom command is applied ,,then forcefield will ignore all the added h-atoms,,,so my question is then it would be a vaccum simulation if the h-atom will be ignored,,secondly the results will be also differnt then when h-atoms are considered. 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] Analysis of sumulation by gromacs.
dear gromacs users.. i have done simulation of my system by gromacs.Now i want to analyse the results by Desmond..i have tried to download it by my official email account for academics version..but it didnt work..if any one of u have its setup ..plz share with me.. thank alot. Mara khan scholar ics,uop. -- 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] simulation of ternary complex
Dear gromacs Users.. I want to simulate ternary complex of protein -DNA -ligand..Is it possible to simulate it combinely? secondly..Gromacs has no graphical interface to visualize results..how can we resolve this issue..Using VMD i have some issues regarding trajectories.. Regards.. Maria khan. ICS,,university of peshawar.. -- 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] Results analysis of gromacs by VMD.
dear gromacs users,, i have done simulation by gromacs and now i want to analyse the results of it by VMD. when i open VMD for drawing RMSD trajectory tool..i dont get graph..and terminal gives me error..that is--ignoring plot..As the plot is not shown by it..i have attached the file and will hv more idea of my problem. thanks for advance .. Maria M.phil scholar. ICS,UOP pakistan. -- 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] trajectory analysis
Dear gromacs users.. I have the following questions. 1) ::how i analyse trajectory using VMD? 2)::Trajectory analysis for overall protein structure stability?? 3)::protein - ligand interaction i-e H-bonds and anyother interactions.?? 4)::trajectory analysis for free energy binding of protein and ligand?? Maria khan M.phil scholar Institute of chemical sciences,,university of peshawar. pakistan -- 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] desmond setup
Dear computational scientist. If anyone of you have worked on desmond for simulation analysis.can you people send me desmond software..As this is a commercial software..and i cant afford it and i need it urgently. Maria khan Mphil scholar institute of chemical sciences university of peshawar. -- 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 _DNA_ligand simulation
dear Justin lemkul. Thanks alot.. You talked about CHARMM36 , bt in ligand -protein manuals of gromacs there is no option for this force field.. while CHARMM27 has been mentioned..is CHARMM36 available now in latest version of gromacs?? secondly ,,the recent forcefield parmbsc1 that u mentioned,which software support this one forcefield.can gmx support it? Regards. Maria khan, M.phil scholar institute of chemical sciences. University of peshawar, Pakistan. -- 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-DNA_ligand simulation.
Dear Gromacs users. Can gromacs is used in Protein -DNA-ligand simulation??f it is used, which forcefield will be used.?? what will be the method for that type of simulation.kindly answer me in detail. regards and thanks Maria khan M.phil scholar institute of chemical sciences. university of peshawar,pakistan. -- 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] Md simulation H-atom trajectory analysis.
Dear justin Thanks for your prompt response. My results are satisfactory.and i managed the H-atoms by _ignh command.but i just want to learn its solution by conventional system of gromacs also thats y i am asking. >From your answer can i say that H-atoms trajectory can be studied either it is handle by -Ignh command or conventional system?? Before your answer i was thinking that by solving the h-atoms by _ignh command i ll not be able to study the H-atom trajectory as the software has ignord it. Thanks for your honorable guidance. -- 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] Md simulation trajectory Analysis.
Dear Justin Lemkul.. Analysing trajectories of Md simulation,,how the H-bonds can be analysed..if after minimization the software has once ignored the H-bonds..?? Secondly how can we rename the H atoms by the gromacs conventional system.Guide me in renaming H atoms of His residue according to conventions? Maria khan regards and thank. -- 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] Md simulation error
Dear justin lemkul,, Thanks alot..i like the way u answer my stupid questions..actually i dont have anyone to guide me except u.thats why i ask even stupid questions.dont mind please.i want to work under your supervision because i have passion for simulation on gromacs. Now coming to the point,,my problem was concerned with his residue of atom HD1.I just went to pdb file and rename that HD1 to H3.then two files formed that are " "posre _protein chain_A.itp and topol_protein_chain _A.itp"" .while topol.top remained empty.now it gives me another error that is " " Residue 'IS A' not found in residue topology database"". im using version 5.1.2 actually. i 'll encourage and wellcome even live discussion with you.I studied your papers on simulation. Regards. GOD bless you. Maria khan -- 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] Md simulation of protein ligand error.
Dear justin.. My problem of protein ligand simulation , regarding protonation states for His residue has solved..now that error exists no more.There are two things that i want to share,,one is that i didnot get how that problem solved,i just followed that manuals while i have no idea how it just solved..secondly it gives furthur another error that says that is "software inconsistancy error"can u kindly guide me please, regards and thanks alot for your coperation. Maria khan. -- 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] Md simulation error..
Dear Justin A. Lemkul, than you so much..i Will follow that link you hv provided..i will concern you for further progress. 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] Md simulation error.
Dear Justin A. Lemkul,,im very much thankful for your honourable response. As i mentioned you that im beginner to use of gromacs,,can you send me all these suggestions in the form of videos,because im not getting you and im confuse.i have followed the manuals of gromacs bt i didnt understand it properly and my background for simulation is not as such strong yet. is there any tuitorials or online course on simulation of proteins and ligand.? 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] Md simulation error
Thanks alot Justin A. Lemkulfor your strong concern. can you please guide me in conforming protonation states for residues.im new user of gromacs for simulation. 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] md simulation by gromacs.
Hello dear gromacs users.. I am running simulation for protein ligand complex that are Glutamate racemase and its inhibitor KRH.Bt it gives me error like" Atom HD1 in residue HIS 61 was not found in rtp entry HISB with 12 atoms while sorting atoms.For a hydrogen, this can be a different protonation state, or it might have had a different number in the PDB file and was rebuilt(it might for instance have been H3, and we only expected H1 & H2).Note that hydrogens might have been added to the entry for the N-terminus.Remove this hydrogen or choose a different protonation state to solve it.Option -ignh will ignore all hydrogens in the input."for making pdb2gmx and it doesnt form topology file. where am i doing wrong. kindly help me out. Regards and thanks. -- 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] Md simulation error
Hello dear gromacs users, i m running md simulation for protein ligand complex that are glutamate racemase and its inhibitor (KRH) bt it gives an error like "Atom HD1 in residue HIS 61 was not found in rtp entry HISB with 12 atomswhile sorting atoms.For a hydrogen, this can be a different protonation state, or itmight have had a different number in the PDB file and was rebuilt(it might for instance have been H3, and we only expected H1 & H2).Note that hydrogens might have been added to the entry for the N-terminus.Remove this hydrogen or choose a different protonation state to solve it.Option -ignh will ignore all hydrogens in the input." where am i doing wrong. kindly help me out Regards and thanks. -- 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.
