[gmx-users] how can i use acpype

hi i want use the amber force field and its need acpype but i got error : acpype -i ref-ligandChimera.mol2 -c user | ACPYPE: AnteChamber PYthon Parser interfacE v. 2014-08-27 18:33:08Z Rev: 7828 (c)

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 128, Issue 74

it is more specific than Re: Contents of gromacs.org_gmx-users digest... Today's Topics: 1. fatal erroe in prorein-ligand comlex (Yaser Hosseini) 2. Re: fatal erroe in prorein-ligand comlex (Justin Lemkul) 3. Re: fatal erroe in prorein-ligand comlex (Justin Lemkul) 4. Re: fatal

[gmx-users] fatal erroe in prorein-ligand comlex

hi gromacs users i got error in step four in protein-ligand complex how can i fix it: Fatal error: number of coordinates in coordinate file (solv.gro, 144131) does not match topology (topol.top, 144171) when i want to ran this: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr

[gmx-users] protein-ligand complex fatal error

hi i just want to run mdrun -v deffnm nvt i run every command in this tutorials http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html but at the end i got two errors : There are: 247500 Atoms Charge group distribution at step 0: 20986 20508 20732 20838

[gmx-users] how can i install sse4.1 and avx_256

hi Reading file md.tpr, VERSION 4.6.5 (single precision) Using 4 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this machine, which is better) how can i use this features for better mdrun speed. thanke you. -- Gromacs Users mailing list * Please search the archive at

[gmx-users] fatal error in gromacs

hi gromacs users when i want to run pdb2gmx command i got a fatal error that said : the residue from MN has lost. and i used all of force feild but i got this error how can i fix it and which one of force feild coomand can i use?? thanke you. -- Gromacs Users mailing list * Please search the

Re: [gmx-users] gromacs-4.6.5 topol file error

directory and has readable permissions, it is impossible to trigger this error. -Justin Sent from my iPad On Sep 25, 2014, at 19:29, Justin Lemkul jalem...@vt.edu wrote: On 9/25/14 9:56 AM, Yaser Hosseini wrote: hi gromacs users i got this error what can i do?? Program pdb2gmx, VERSION

[gmx-users] grompp help

hi gromacs user i have problem with grompp command in gromacs i cant find .mdp files and i cant pass step 4 in this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme_old/04_ions.html im new in gromacs please help me to find a way to fix my problems.

[gmx-users] gromacs-4.6.5 topol file error

hi gromacs users i got this error what can i do?? Program pdb2gmx, VERSION 4.6.5 Source code file: /build/buildd/gromacs-4.6.5/src/gmxlib/futil.c, line: 593 File input/output error: 1AKI.pdb For more information and tips for troubleshooting, please check the GROMACS website at

[gmx-users] gromacs command grompp error

hi gromacs users i wanted to run this command : grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr but i dont have this file in my folder path: ions.mdp how can i get this file in my path. thank you. -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] gromacs command grompp error

thanks. On 9/25/14, Yaser Hosseini yaser.hosseini.biolog...@gmail.com wrote: hi gromacs users i wanted to run this command : grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr but i dont have this file in my folder path: ions.mdp how can i get this file in my path. thank you

[gmx-users] error in running pdb2gmx

hi gromacs users -- 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

[gmx-users] gromacs error

hi guys i have a problems with gromacs command .how can i can solve this problems: i install gromacs and i dont know what can i do: gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top No command 'gmx' found, did you mean: Command 'gcx' from package 'gcx' (universe)