[gmx-users] atb topology files

hi, i want to ask which files should be selected when ligand topology is generated by prodrg server? and do they need also modification regards kalsoom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://w

[gmx-users] ligand topology error

hi, whenever, i Submit the molecule to ATB ( http://compbio.biosci.uq.edu.au/atb/index.py) FOR BUILDING THE TOPOLOGY OF LIGAND, IT SAYS Your job that was submitted at 2013-02-01 00:56:07 (RNME = _NGD) had at least one error. Specifically, the QM calculation failed. The most likely cause is that e

[gmx-users] acpype command not found

hi, when i run the comand acpype -i lig.pdb it says command not found even i have installed latest version of groamcs, what to do ? regards kalsoom -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www

[gmx-users] bad box error

hi , when i use "editconf" to generate a dodecahedron box with the command editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0 the output shows the warning bad box in file generated a new cubic box 9.213 x2.495 x2.960 what is the mean of "bad box in file"? and why editconf

[gmx-users] error

hi, i am using the following comamnd pdb2gmx -ff amber99sb -f proteinamber.pdb -o protei2.pdb -p protein.top -water spce -ignh and gets the error Fatal error: Residue 2 named GLU of a molecule in the input file was mapped to an entry in the topology database, but the atom CG used in that entr

[gmx-users] protein topology file fetal error

hi all, i am new to gromacs, when i run my protein file by following the tutorial example mention here( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html) I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE.. * Fatal error: Atom HA in residue SE