On Tue, Dec 18, 2018 at 12:17 AM Sri Prasanth Ghanta, Doctoral Research Scholar, Biosciences, SSSIHL <prasanthgha...@sssihl.edu.in> wrote:
> Dear all, > > I have started following the new tutorial > <http://www.mdtutorials.com/gmx/complex/index.html> and the old tutorial > < > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex_old/index.html > > > to carryout the simulation of JZ4 with Lysozyme. > I was unable to run the cgenff script as I am not aware of setting up > microenvironment in Ubuntu to run older python version, which is essential > in running the script required for creation of ligand topology. > > From a bit of reading, I understood that ATBserver is preferred over PRODRG > as the topology created is more accurate. > I had followed the tutorial to build the complex (complex.gro) by > incorporating jz4.gro (from ATBserver) in the 3htb_processed.gro. I had > also incorporated the ligand topolgy (jz4.itp) into the topol.top as > instructed. > I was successful in building the box and solvating. However, when i try to > run > gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr > I get an error in line 1345 stating, > ----- > > *Fatal error:* > *Atomtype CAro not found* > > *------* > I am assuming it's something to do with the representation of the carbon > (aromatic) in the topology of the ligand (jz4.itp), which reads like this.. > ----------------------------------------- > [ moleculetype ] > ; Name nrexcl > WX56 3 > [ atoms ] > ; nr type resnr resid atom cgnr charge mass > 1 CH3 1 WX56 C1 1 -0.011 15.0350 > 2 CH2 1 WX56 C2 2 0.028 14.0270 > 3 CH2 1 WX56 C3 3 0.113 14.0270 > 4 CAro 1 WX56 C4 4 -0.194 12.0110 > 5 CAro 1 WX56 C9 5 0.338 12.0110 > 6 OAlc 1 WX56 O1 6 -0.588 15.9994 > 7 HS14 1 WX56 H12 7 0.428 1.0080 > 8 CAro 1 WX56 C8 8 -0.268 12.0110 > 9 HC 1 WX56 H11 9 0.167 1.0080 > 10 CAro 1 WX56 C7 10 -0.100 12.0110 > 11 HC 1 WX56 H10 11 0.131 1.0080 > 12 CAro 1 WX56 C6 12 -0.201 12.0110 > 13 HC 1 WX56 H9 13 0.136 1.0080 > 14 CAro 1 WX56 C5 14 -0.124 12.0110 > 15 HC 1 WX56 H8 15 0.145 1.0080 > ; total charge of the molecule: -0.000 > ------------ > > However, I am not sure, which code I need to use in the place of CAro, OAlc > and HS14. Can you please help me in this regard? > P.S: I am trying to use GROMOS96 54a7 forcefield for this purpose. > > Are you trying to combine this ligand topology with the CHARMM protein topology generated in the tutorial? If so, that's fundamentally incorrect and you can never make that work. If you're doing things entirely within the context of GROMOS, then you likely need additional files from the ATB server that provide parameters for the "unknown" atom types. -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.