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

i did it but i get this error again. Sent from my iPad > On Sep 25, 2014, at 19:29, Justin Lemkul wrote: > > > >> On 9/25/14 9:56 AM, Yaser Hosseini wrote: >> hi gromacs users >> >> i got this error what can i do?? >> >> Program pdb2gmx,

Re: [gmx-users] grompp help

thank you for replay when i want to download this file and i click on it its nothing happend and just the text page opend and its nothing to download. Sent from my iPad > On Sep 26, 2014, at 19:56, Justin Lemkul wrote: > > > >> On 9/26/14 12:23 PM, Yaser Hosseini wr

Re: [gmx-users] grompp help

thank you i did it. Sent from my iPad > On Sep 26, 2014, at 23:42, Justin Lemkul wrote: > > > >> On 9/26/14 12:50 PM, yaser wrote: >> thank you for replay >> >> when i want to download this file and i click on it its nothing happend and >> j

[gmx-users] add Mn in itp file

hi i tried add Mn in .itp file but its need some information such as sigma and epsilon and i search for find this but i cant find this parameters .anyone knows any things about how can i add Mn in .itp file and if you know any tutorials articles about add ions . thanke you. Sent from my iPho

[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) Comm

[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 https://maillist.sys.kth.se/mailman/listi

[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 http://www.gromacs

[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 http://www.gromacs.

Re: [gmx-users] gromacs command grompp error

thanks. On 9/25/14, Yaser Hosseini 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. &

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

i dont know how can create ions.mdp file for grompp command in gromacs . where can i found it?? On Thursday, September 25, 2014 11:14 PM, Justin Lemkul wrote: On 9/25/14 2:15 PM, yaser wrote: > i did it but i get this error again. > If the file is, in fact in the working directo

[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. thank

[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

[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] protein-ligand complex fatal error

hi gromacs users i want to run Protein-Ligand Complex but when i want to run this command : mdrun -deffnm nvt i got this error Fatal error: 4 particles communicated to PME node 2 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x. This

[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] 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

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

...@maillist.sys.kth.se > > When replying, please edit your Subject line so 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 er

[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) 2