Re: [gmx-users] generation of gro file

2013-08-18 Thread Musharaf Ali
Dear Justin Thanks a lot. will definitely do it. warm regards On Sun, Aug 18, 2013 at 10:53 AM, Musharaf Ali wrote: > Dear Justin > Again thanks. Actually the problem arises in the running of pdb2gmx of pdb > file of crown ether. I have generated the pdb file from xyz coordinates > using openb

Re: [gmx-users] generation of gro file

2013-08-18 Thread Justin Lemkul
On 8/18/13 1:23 AM, Musharaf Ali wrote: Dear Justin Again thanks. Actually the problem arises in the running of pdb2gmx of pdb file of crown ether. I have generated the pdb file from xyz coordinates using openbabel. The pdb file looks like below. COMPND D:\data-structure\18c6.xyz AUTHOR GENE

Re: [gmx-users] generation of gro file

2013-08-17 Thread Musharaf Ali
Dear Justin Again thanks. Actually the problem arises in the running of pdb2gmx of pdb file of crown ether. I have generated the pdb file from xyz coordinates using openbabel. The pdb file looks like below. COMPND D:\data-structure\18c6.xyz AUTHOR GENERATED BY OPEN BABEL 2.3.2 HETATM 1 O LIG 1

Re: [gmx-users] generation of gro file

2013-08-17 Thread Justin Lemkul
On 8/17/13 10:58 AM, Musharaf Ali wrote: Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. I don't know. I seem to recall some discussion about .xyz files some time ago, but I forget the outcome. My point was tha

Re: [gmx-users] generation of gro file

2013-08-17 Thread Musharaf Ali
Thank You Justin But you mean to say that even XYZ coordinates like below format (18-crown-6) can be directly used in Gromacs. O 0.00 0.00 0.00 C 0.00 0.00 1.40 C 1.367075 0.00 1.883328 H -0.513360 0.889165 1.763000 H -0.513360 -0.889165 1.763000 H 1.367079 0.0

Re: [gmx-users] generation of gro file

2013-08-17 Thread Justin Lemkul
On 8/16/13 10:50 PM, Musharaf Ali wrote: Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. The specifications of the .gro format are described here: http://manual.gromacs.org/online/gro.html Note that there is no requirement to u

[gmx-users] generation of gro file

2013-08-16 Thread Musharaf Ali
Hi could somebody help how to generate grow file from xyz coordinates specially for crown ether type molecules. Here the xyz coordinates are attached for 18-crown-6. Thank in advance. Regards New learner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/g