[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

[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

[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. --

[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

[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

[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

[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??

[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

[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

[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

[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

[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

[gmx-users] trajectory analysis

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

[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

[gmx-users] protein _DNA_ligand simulation

,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

[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

[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

[gmx-users] Md simulation trajectory Analysis.

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

[gmx-users] Md simulation error

quot; 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 ar

[gmx-users] Md simulation of protein ligand error.

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

[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

[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

[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

[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

[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