Re: [gmx-users] Topology

Hi, You already have the topology for it :-) Chirality is about spatial configuration, topologies are about connectivity. There's no need to try to encode the spatial configuration because there is no accessible path for the conversion, given the existence of the bonded parameters.

[gmx-users] Topology

Dear Gromacs Users, My molecule has a chiral center and I have topology for that configuration. I would like to know how do we get the topology for the opposite configuration in gromacs? Thank you. -- Best Regards Shan Jayasinghe -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Obtaining AMBER parameter for Zwitterion Amino acids to use in Gromacs

Hi, I have found a AMBER database which contains the parameters for zwitterion amino acids from the link below: http://research.bmh.manchester.ac.uk/bryce/amber/ Does anyone know how to extract the parameters to use in Gromacs? Akash -- Gromacs Users mailing list * Please search the

Re: [gmx-users] [gmx-user] advantage of charmm force field over opls for protein md simulation and protein+Inhibitor md simulation

On 8/25/19 4:55 PM, Quin K wrote: Hi, 1. Are there any advantages of charmm forcefield over opls-all atom ff, for protein md simulation and protein+Inhibitor md simulation? This decision is one only you can (and should) make after an examination of relevant literature. What have studies

[gmx-users] [gmx-user] advantage of charmm force field over opls for protein md simulation and protein+Inhibitor md simulation

Hi, 1. Are there any advantages of charmm forcefield over opls-all atom ff, for protein md simulation and protein+Inhibitor md simulation? 2. Where can i find parameter files (.mdp files) for charmm 22 forcefield for gromacs? 3. Can CHARMM27 all-atom force field (CHARM22 plus CMAP for

Re: [gmx-users] (no subject)

On 8/25/19 2:17 PM, Navneet Kumar Singh wrote: Yeah! I have read that. uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in Since you are getting an error rather than a warning, that means you are not using GROMACS 2016.x, as the instructions I pointed to you say.

Re: [gmx-users] (no subject)

Yeah! I have read that. uses -maxwarn 1 to produce .tpr file using grompp command as mentioned in python script cgenff_charmm2gmx_py2.py output of cgenff_charmm2gmx_py2.py

Re: [gmx-users] (no subject)

On 8/25/19 11:49 AM, Navneet Kumar Singh wrote: Thank You Sir! Attached file can be downloaded from following link. https://fil.email/OR7Nsh0f Error ERROR 1 [file unk.itp, line 497]:

Re: [gmx-users] (no subject)

Thank You Sir! Attached file can be downloaded from following link. https://fil.email/OR7Nsh0f Error ERROR 1 [file unk.itp, line 497]: Duplicate atom index (23) in virtual_sites3

Re: [gmx-users] Should Cation Ligand be removed before MD simulaiton

On 8/25/19 10:06 AM, Quin K wrote: Hi I'm hoping to use a protein for MD simulation and later for docking with Autodock vina. *However there is a Mg2+ cation ligand in the DPB crystal structure of protein. Should this be removed before MD simulation? *and replaced with lets say Na+ to keep

Re: [gmx-users] (no subject)

On 8/25/19 8:33 AM, Navneet Kumar Singh wrote: can you please help in solving this error while running MD simulation of protein-ligand complex using CHARMM36 force field on GROMACS engine. *Command* *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr* *ERROR* *ERROR 1 [file

[gmx-users] Should Cation Ligand be removed before MD simulaiton

Hi I'm hoping to use a protein for MD simulation and later for docking with Autodock vina. *However there is a Mg2+ cation ligand in the DPB crystal structure of protein. Should this be removed before MD simulation? *and replaced with lets say Na+ to keep the charge of protein zero. I'm hoping

[gmx-users] (no subject)

can you please help in solving this error while running MD simulation of protein-ligand complex using CHARMM36 force field on GROMACS engine. *Command* *gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr* *ERROR* *ERROR 1 [file unk.itp, line 497]: Duplicate atom index (23) in