Re: [gmx-users] MD on docked complex using AMBER FF

2010-09-20 Thread manoj singh
First, you have to develop parameter for your molecule withing Amber. Then you have to create .prmtop and .inpcrd files for your molecule, and than you can convert the Amber topology to Gromacs topology. You will need AmberTools and a script called amb2gmx.pl. Following links would be helpful for

[gmx-users] PBS script

2010-09-12 Thread manoj singh
Hi, I will be very thankful if someone can share a sample pbs script for running Gromacs-4.5. Thanks! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before po

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
Thanks for the reply! I will be very thankful if you can send me whatever you have. I will change that according to my system. On Sun, Sep 12, 2010 at 5:09 PM, Justin A. Lemkul wrote: > > > manoj singh wrote: > >> Hi, >> >> I will be very thankful if someone

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
Thanks for reminding me the existence of Google. It must be hard to copy and paste few lines of the PBS script than advertising the Google. On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul wrote: > > > manoj singh wrote: > >> Thanks for the reply! >> >> I will be

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
Google given a link to very good site in regard. http://biowulf.nih.gov/apps/gromacs/ On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul wrote: > > > manoj singh wrote: > >> Thanks for the reply! >> >> I will be very thankful if you can send me whatever you

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
r own research > > On Sep 12, 2010, at 5:52 PM, manoj singh wrote: > > Thanks for reminding me the existence of Google. > It must be hard to copy and paste few lines of the PBS script than > advertising the Google. > > On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul wr

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
anks for reminding me the existence of Google. > It must be hard to copy and paste few lines of the PBS script than > advertising the Google. > > On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul > wrote: > > >> >> manoj singh wrote: >> >> Thanks for the r

Re: [gmx-users] PBS script

2010-09-12 Thread manoj singh
compiled with mpich2), which I hope to fix tomorrow. So, please conclude this topic here. Sincerely, On Sun, Sep 12, 2010 at 10:33 PM, Justin A. Lemkul wrote: > > > manoj singh wrote: > >> Hi Chris, >> >> >> Sorry if I have been rude is my response. >&