Re: [gmx-users] error in grompp step

Dear Mark sir, Thank you... I will try with the later versions. I am actually using modified version of gromacs-4.6.2[by J S Hub et al.,] , for calculating swaxs(small and wide angle x ray scattering) profiles and swaxs driven MD. I will learn to incorporate swaxs driven MD to later versions with

Re: [gmx-users] error in grompp step

Hi, You should probably also avoid using software that is five years old and no longer supported with bug fixes... Mark On Tue, Mar 20, 2018 at 6:09 AM Upendra N wrote: > Dear Justin sir, > > Thank you very much I tried that also but same errors were coming. > > I

Re: [gmx-users] error in grompp step

Dear Justin sir, Thank you very much I tried that also but same errors were coming. I will try it out again sir With Regards Upendra N -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post?

[gmx-users] Error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

Re: [gmx-users] error in grompp step

On 3/19/18 10:05 AM, Upendra N wrote: Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp

[gmx-users] error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

[gmx-users] error in grompp step

Dear gromacs users, I am doing protein-Ligand simulation using gromacs-4.6.2 with charmm36 forcefield. I have generated protein topology using pdb2gmx and ligand topology using the CGenFF-webservice and cgenff_charmm2anton.py (to convert *.str to *.itp and cordinates)

Re: [gmx-users] ERROR IN GROMPP

On 1/12/17 8:19 AM, Subashini .K wrote: Hi gromacs users, I got an error when the following command gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em The corresponding em.mdp was ; to test ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v ; mdrun -v -deffnm

Re: [gmx-users] error running grompp for ions.mdp input

kth.se < gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Ghada Mhmd <ghada.mhm...@gmail.com> Sent: Tuesday, February 16, 2016 8:19 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] error running grompp for ions.mdp input hello I'm new to gromacs I'm si

Re: [gmx-users] error running grompp for ions.mdp input

February 16, 2016 8:19 AM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] error running grompp for ions.mdp input hello I'm new to gromacs I'm simulating a protein in a mixed solvent (water/organic solvent) *first I added my organic solvent molecule (Methanol) using gmx inse

[gmx-users] error running grompp for ions.mdp input

hello I'm new to gromacs I'm simulating a protein in a mixed solvent (water/organic solvent) *first I added my organic solvent molecule (Methanol) using gmx insert-molecules command *then I solvate it in water using gmx solvate command but I went to adding atom using gmx grompp command

Re: [gmx-users] Error using grompp - atomtype not found

...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, May 25, 2015 7:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error using grompp - atomtype not found On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos

Re: [gmx-users] Error using grompp - atomtype not found

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Monday, May 25, 2015 7:34 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Error using grompp - atomtype not found On 5/25

[gmx-users] Error using grompp - atomtype not found

Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_ not found. I have added all the needed atoms in atomtypes.atp of the ff I

Re: [gmx-users] Error using grompp - atomtype not found

On 5/25/15 11:08 AM, Sotirios Dionysios I. Papadatos wrote: Hi, I have made a molecule.itp, which is what I want to run MD calculations on. Meaning I couldn't produce it with pdb2gmx but I rather made a .top with vi editor. When I try to use grompp it says atomtype opls_ not found. I

Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx

Yaap.. that was the mistak you were doing. On Thu, Apr 16, 2015 at 4:50 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Abhijit, Thank you infact I myself figured out that now; while solvating I used spc216.gro instead of tip4 water model and the error now gone. Sorry for the trouble.

Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx

How did you solvate your system? What exact command did you use? On Thu, Apr 16, 2015 at 2:37 PM, Raj D gromacs.fo...@gmail.com wrote: Dear Users, I want to use TIP4P-Ew water model for my simulation of protein. Every time I select water model TIP4P-Ew option number 3 in pdb2gmx step it

Re: [gmx-users] error in grompp if used TIP4p-Ew water at pdb2gmx

Dear Abhijit, Thank you infact I myself figured out that now; while solvating I used spc216.gro instead of tip4 water model and the error now gone. Sorry for the trouble. Regards, Raja On Apr 16, 2015 4:10 PM, abhijit Kayal abhijitchemi...@gmail.com wrote: How did you solvate your system? What

Re: [gmx-users] error in grompp : No such molecule type Protein

On 3/16/15 6:35 AM, Antara mazumdar wrote: Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running

[gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro

Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting *Something is wrong in the

[gmx-users] error in grompp : No such molecule type Protein

Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running grompp i am getting No such molecule type

Re: [gmx-users] error in grompp : Something is wrong in the coordinate formatting of file system.gro

On 3/16/15 7:12 AM, Antara mazumdar wrote: Hi, I am trying to minimise a coarse grained system having DOPC lipid bilayer, a dimeric protein and water. The mdp file has DOPC, Protein and W as coupling groups and my topology file also mentions the number of each correctly. However while running

Re: [gmx-users] error in grompp command

: -- Message: 2 Date: Wed, 2 Jul 2014 12:26:07 +0530 From: RINU KHATTRI nickname.mi...@gmail.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua

Re: [gmx-users] error in grompp command

wrote: -- Message: 2 Date: Wed, 2 Jul 2014 12:26:07 +0530 From: RINU KHATTRI nickname.mi...@gmail.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID

Re: [gmx-users] error in grompp command

mailto:gromacs.org_gmx-users-requ...@maillist.sys.kth.se wrote: -- Message: 2 Date: Wed, 2 Jul 2014 12:26:07 +0530 From: RINU KHATTRI nickname.mi...@gmail.commailto: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users

Re: [gmx-users] error in grompp command

On 7/3/14, 6:27 AM, RINU KHATTRI wrote: hello gromacs users now have been removed this error after changing the number of SOL in topol_popc.top file (counted from popc128.gro) after that i hav used -maxwarn 1 command result is Generated 813 of the 2346 non-bonded parameter combinations

[gmx-users] error in grompp command

hello gromacs i an working on protein ligand complex with lipid membrane (popc) grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1 after this fatal error atomtypes CA not found and only md.oonly mdout is formed kindly help -- Gromacs Users mailing list * Please search

[gmx-users] error in grompp command

...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.commailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 hello gromacs i an working on protein ligand complex

Re: [gmx-users] error in grompp command

: nickname.mi...@gmail.com To: gmx-us...@gromacs.orgmailto:gmx-us...@gromacs.org Subject: [gmx-users] error in grompp command Message-ID: caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com mailto:caoefx3kbphak_brp4l4orcp_gsbsusohnlughx0wyjwewua...@mail.gmail.com Content-Type: text

Re: [gmx-users] Error in grompp for protein-ligand tutorial

On 1/27/14, 2:15 PM, José Adriano da Silva wrote: I am new to Gromacs, then follow the tutorial protein-ligand, decided to adapt the procedure for my protein (acetylcholinesterase) and my binder. The procedure is this (protein-ligand complex):

[gmx-users] Error in grompp for protein-ligand tutorial

I am new to Gromacs, then follow the tutorial protein-ligand, decided to adapt the procedure for my protein (acetylcholinesterase) and my binder. The procedure is this (protein-ligand complex): http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp lex/index.html