Re: [gmx-users] charmm gui pdb to gro

*thanks sahil * *but i am interested in lipid molecule conversion not protein. I think pdb2gmx will work for protein molecules only.* -- 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

Re: [gmx-users] charmm gui pdb to gro.

Hey, You could use pdb2gmx on the CHARMM-GUI ".pdb" output. The -ignh flag allows for ignoring preexisting hydrogen atoms if that's really required. Cheers, Sahil On 2020-01-14 12:23, Yogesh Sharma wrote: > Greetings, > hey, I want to convert the charmm gui generated pdb (membrane +

[gmx-users] charmm gui pdb to gro.

Greetings, hey, I want to convert the charmm gui generated pdb (membrane + protein) to gromacs readable file. charmm generated lipids contain hydrogen atoms and naming differences. I tried doing it manually but couldnt succeed. Is there any script available for atom renaming and reordering? I

Re: [gmx-users] CHARMM GUI membrane builder's assembled output

On 9/19/19 2:24 PM, Yogesh Sharma wrote: Greetings, I used charmm gui's custom Membrane/protein builder to assemble components for MD simulation. It gave me equillibriated box. I am confused whether I should equllibriate box again or not? From which step should I start in Gromac,Energy

[gmx-users] CHARMM GUI membrane builder's assembled output

Greetings, I used charmm gui's custom Membrane/protein builder to assemble components for MD simulation. It gave me equillibriated box. I am confused whether I should equllibriate box again or not? From which step should I start in Gromac,Energy minimization, equillibriation or Production MD? --

Re: [gmx-users] Charmm-Gui output to Gromacs

On 5/4/18 5:35 AM, Mark Abraham wrote: Hi, Charmm-GUI writes GROMACS files natively, doesn't it? It does. I haven't run the Glycan Reader directly but it is embedded as a component of the Quick MD Simulator, which gives all necessary GROMACS input files (coordinates, topology, and .mdp).

Re: [gmx-users] Charmm-Gui output to Gromacs

Hi, Charmm-GUI writes GROMACS files natively, doesn't it? Mark On Fri, May 4, 2018 at 10:16 AM Frederic Schneider < frederic.schnei...@tu-bs.de> wrote: > Hello everyone, > > i would like to convert the topology files from the output of the > Charmm-Gui/Glycan Reader(.psf file) to the Gromacs

[gmx-users] Charmm-Gui output to Gromacs

Hello everyone, i would like to convert the topology files from the output of the Charmm-Gui/Glycan Reader(.psf file) to the Gromacs format (.itp, .top). Is there a preferred script or program to do this task? Best regards, Frederic Frederic Schneider, M.Sc. TU Braunschweig Institut für

[gmx-users] charmm-gui

Dear Justin,Can I use the charmm-gui output file for peptide (.itp file) as an input file for GROMACS, and instead of one peptide, I set 4 peptides in the bulk of water and near the head groups?In fact , I want to extract manually peptide from the final .gro file containing peptide + lipids +

Re: [gmx-users] charmm-gui

On 4/4/18 4:49 PM, m g wrote: Dear Justin, I am using charmm-gui to generate the lipid bilayer according to CHARMM36 force field. I embed the peptide in bilayer. Is the file produced for peptides, which is based on the CHARMM36, can be used in simulation with GROMACS(because I want to used

[gmx-users] charmm-gui

Dear Justin, I am using charmm-gui to generate the lipid bilayer according to CHARMM36 force field. I embed the peptide in bilayer. Is the file produced for peptides, which is based on the CHARMM36, can be used in simulation with GROMACS(because I want to used 4 peptide in my bilayer)? Can I

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Ok I will. Thank you very much Justin. > On 02 Sep 2016, at 16:58, Justin Lemkul wrote: > > > > On 9/2/16 10:44 AM, Justin Lemkul wrote: >> >> >> On 9/2/16 10:43 AM, gozde ergin wrote: >>> Ok I understand. I did exactly same thing for another molecule (SDS) and >>>

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

On 9/2/16 10:44 AM, Justin Lemkul wrote: On 9/2/16 10:43 AM, gozde ergin wrote: Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. If you upload a tarball of all the

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

On 9/2/16 10:43 AM, gozde ergin wrote: Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. If you upload a tarball of all the GROMACS files provided by CHARMM-GUI, I will

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Ok I understand. I did exactly same thing for another molecule (SDS) and everything is working without any error. But I do not know what should I do with cis-pinonic. > On 02 Sep 2016, at 16:40, Justin Lemkul wrote: > > > > On 9/2/16 10:39 AM, gozde ergin wrote: >> Hi

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

On 9/2/16 10:39 AM, gozde ergin wrote: Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

Hi Justin, I try to use the CHARMM-GUI files directly. My purpose is simulating the water and ci-pinonic system. Cis-pionic molecules will stay on the water surface and I would like to estimate surface tension reduction. What should I change in CHARMM-GUI files? > > CHARMM-GUI provides a

Re: [gmx-users] CHARMM-GUI files give error in Gromacs

On 9/2/16 10:28 AM, gozde ergin wrote: Dear all, I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid. After that I used genbox command of gromacs and add some water molecules. When I try to run I get 100 Errors saying : No default bond types, No default U-B types,

[gmx-users] CHARMM-GUI files give error in Gromacs

Dear all, I used CHARMM-Gui and prepared the .pdb, .itp and .top file for cis pionic acid. After that I used genbox command of gromacs and add some water molecules. When I try to run I get 100 Errors saying : No default bond types, No default U-B types, No default Proper Dih. types, No default

Re: [gmx-users] CHARMM-GUI Membrane building problems

Message: 5 Date: Fri, 6 May 2016 06:51:55 -0400 From: Justin Lemkul<jalem...@vt.edu> To:gmx-us...@gromacs.org Subject: Re: [gmx-users] CHARMM-GUI Membrane building problems Message-ID:<7d29cbd8-6111-3a02-eddf-9f5e77d22...@vt.edu> Content-Type: text/plain; charset=windows-1252; f

Re: [gmx-users] CHARMM-GUI Membrane building problems

On 5/5/16 11:41 AM, John Smith wrote: Hello, I am resending this message from my Gmail account, as it appears that messages sent from my Yahoo account are going to spam. Apologies if you have already seen this. I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with CHARMM-GUI. The

[gmx-users] CHARMM-GUI Membrane building problems

Hello, I am resending this message from my Gmail account, as it appears that messages sent from my Yahoo account are going to spam. Apologies if you have already seen this. I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with CHARMM-GUI. The process seems to be fairly

[gmx-users] CHARMM-GUI Membrane building problems

Hello All, I am trying to build a simple DOPC-DPPC-Cholesterol bilayer with CHARMM-GUI. The process seems to be fairly straightforward. Unfortunately, there are problems with the resulting configuration of the membrane. After running the equilibration scripts provided as part of the Charmm-GUI

[gmx-users] Charmm gui error when making topology

Dear all, im trying to make topology for few ligands,(CHARMM ff)when i try to run it end with error i made unique name for all atoms using VMD-molfacature tool and used Discovery studio,open babel to convert to mol2 file for uploading to charmm-gui im getting following error awk: cmd. line:1:

Re: [gmx-users] Charmm gui error when making topology

On 12/30/15 9:21 AM, Nikhil Maroli wrote: Dear all, im trying to make topology for few ligands,(CHARMM ff)when i try to run it end with error i made unique name for all atoms using VMD-molfacature tool and used Discovery studio,open babel to convert to mol2 file for uploading to charmm-gui

[gmx-users] CHARMM-GUI: new features for GROMACS

Hi All, I am pleased to announce that the CHARMM-GUI team has extended the capabilities of CHARMM-GUI (www.charmm-gui.org) to provide GROMACS topologies, .mdp files, and run scripts as part of the standard output of CHARMM-GUI. That is, one can now assemble a system (even heterogeneous