Thanks Justin. How should I check if there is a Ter between protein and glucose ? If I get you right, for my protein and Bglc system I just need the Bgc in the .pdb to be changed to Bglc. Do I need to seprate Bglc from the protein and follow the tutorial or can it be regarded as a complex of protein-ligand and I can go ahead with pdb2gmx -f .pdb ? I tried pdb2gmx and got this error : there were 233 missing atoms in molecule other, if you want to use this incomplete topology anyhow use the option -missing. I continued with the-missing flag but there built an incomplete topology. In the energy minimizationit stops with the : 'simulation ended prematurely no perrformance report will be written'. Should I continue regardless of the incomplete topology and this message ? On Monday, February 25, 2019, 7:10:35 PM EST, Justin Lemkul <jalem...@vt.edu> wrote:
On 2/25/19 4:26 PM, mary ko wrote: > Thank you Justin. I am actually following the protein-ligand tutorial to do >simulations of my protein-ligand system. I skipped the python >cgenff_charmm2gmx.py... Because of the mismatch of cgenff error couldnt be >fixed. I have the bgc which is beta-D-glucose and built its .gro file as a >ligand and protein-processed.gro and I copied the ligand in the >protein-processed.gro to have the complex.gro. I also use charmm36-nov2018 and >added it in the force fields with the Bglc to Bgc change in merged.rtp. Now >that I try to build the topology.top file with pdb2gmx or even x2top there is >an error: atom ot1 in residue Phe was not found in rtp entry Phe with 20 atoms >while sorting atoms for pdb2gmx and could only find a force field type for >19078 out of 21750 atoms for x2top. What do you think I should do to build the >topology?Thanks. If you have a protein with BGLC as the ligand, use pdb2gmx and make sure there is a TER between the protein and glucose, or otherwise a change in chain identifier. Do not use x2top and do not modify merged.rtp (modify the residue names in the PDB file instead). -Justin > On Saturday, February 23, 2019, 6:50:39 PM EST, Justin Lemkul ><jalem...@vt.edu> wrote: > > > > On 2/20/19 11:19 AM, mary ko wrote: >> Dear all, >> I face the 'Residue BGC not found in the database' error when I try to build >> the topology file of my protein-ligand system by pdb2gmx -f pro.pdb. I used >> Charmm force field but I tried it with all the other force fields as well to >> see if the problem could be solved which was useless. I searched the list >> and errors-gromacs in the website and found that the simplest way is to >> change the name of this residue. As I am not familiar with protein >> structure, I do not know what changes may be helpful to pass this error. >> also, it is said that one way is to parameterize the residue which I do not >> know how to do that. Your help would be highly appreciated.Thanks! > If "BGC" is a synonym for beta-D-glucose, that is called BGLC in CHARMM, > so you just need to rename the residue accordingly. If it is some other > unknown species, then yes, you need to parametrize it yourself. > > -Justin > -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.