yes i am following this tutorial too this is my topology file for the ligand i made by atb
*http://compbio.biosci.uq.edu.au/atb/download.py?molid=7045 * *from here i got the .itp file and optimzed ligand.pdb file but what about the .gro file and .top file * *i ran that command to make the .gro and .top file of ligand .... * *this is as follows * pdb2gmx -f my_ligand_opt.pdb -o my_ligand.gro -i my_ligand_posre.itp -p my_ligand.top. this generated the fetal error Fatal error: Residue 'LIG' not found in residue topology database SO WHAT SHOULD I DO ABOUT THIS PROBLEM On Tue, Feb 19, 2013 at 5:58 PM, Justin Lemkul <[email protected]> wrote: > > > On 2/19/13 4:23 AM, amna khan wrote: > >> hi all, >> >> i generated the .itp file for my ligand using ATB, >> and i have generated the protein topology file by using the forcefield 13 >> >> my question is i need to generate the *ligand .top and .gro files* >> >> >> and when i use the command >> >> >> *pdb2gmx -f lig.pdb -o igand.gro -i lig.itp -p iig.top >> >> * >> *the error arises that >> >> Fatal error: >> Residue 'LIG' not found in residue topology database >> >> >> * >> what should i do ? >> >> how to create the rtp file for my ligand ... i have read the tutorail but >> i >> am not getting it what steps* exactly should i do please please help me >> and >> >> guide me in making the .rtp file for my ligand >> * >> >> > Chapter 5 of the manual describes .rtp format, but you don't need it. You > already have a ligand topology from ATB, so why ask pdb2gmx to do it over > again? Remove the ligand from the coordinate file and deal with it > separately. I don't know which tutorial you're referring to, but you > should at least try to follow the protocol I describe here: > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** > gmx-tutorials/complex/index.**html<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html> > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
