Re: [gmx-users] .XYZ file format to .gro format

2017-10-18 Thread Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL
As Justin pointed out in GROMACS per se we can't convert .xyz to .gro file. On 19-Oct-2017 1:32 AM, "Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL" wrote: I can think of an option If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'.

Re: [gmx-users] .XYZ file format to .gro format

2017-10-18 Thread Dr. K N Naresh, Post-Doctoral Fellow, Biosciences, SSSIHL
I can think of an option If it is a small molecule, .xyz can be converted to .pdb using 'OpenBabel'. And .gro file can be generated for the .pdb using PRODRG server online. I guess even directly using the .xyz file, PRODRG can generate .gro file. Best Naresh On 18-Oct-2017 8:53 PM, "Justin

Re: [gmx-users] .XYZ file format to .gro format

2017-10-18 Thread Justin Lemkul
On 10/18/17 11:01 AM, Nagasree Garapati wrote: Hi I have structure of a molecule in .xyz format, is there an option similar to pdb2gmx in gromacs to convert .xyz file to .gro files? Format conversion is done with editconf or trjconv; the fact that one gets a coordinate file at the end of