On 1/31/19 11:48 PM, Anjali Patel wrote:
Hello users, I know there are lots of discussion on this topic and i have gone through all those even whole chapter 5 also. but didn’t get any solution or where i am wrong. i want to generate .tpr file. i am using gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr. in that i have generated CNT topology file by this http://chembytes.wikidot.com/grocnt and molecule topology file taken by Automated topology builder (ATB) now i have merged both file and .top files is here, ; Include forcefield parameters #include "./cnt.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl CNT 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 CJ 1 UNK C1 1 0 12.011 ; qtot 0 2 CJ 1 UNK C2 2 0 12.011 ; qtot 0 3 CJ 1 UNK C3 3 0 12.011 ; qtot 0 4 CJ 1 UNK C4 4 0 12.011 ; qtot 0 ....... #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include forcefield parameters #include "./oplsaa.ff/forcefield.itp" ; Include ligand topology #include "drug.itp" ; Include topology for ions #include "./oplsaa.ff/spc.itp" ; Include water topology #include "oplsaa.ff/tip3p.itp" [ system ] ; Name CNT in water [ molecules ] ; Compound #mols CNT 1 _JDN 1 SOL 2515 where drug.itp is below ; Include forcefield parameters #include "./oplsaa.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl _JDN 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass typeB chargeB massB 1 opls_236 0 _JDN O14 0 -0.500 15.99940 2 opls_145 0 _JDN C41 1 0.000 12.01100 3 opls_145 0 _JDN C42 2 0.000 12.01100 4 opls_145 0 _JDN C47 3 -0.115 12.01100 5 opls_146 0 _JDN H51 3 0.115 1.00800 ............ opls_236 and all atom types are already in .rtp, .atp and ffnonbonded.itp file. i am not getting the issue. as it is very urgent for me Thanks in advance for any advice and suggestions
You're mixing force fields. You've got one component that uses OPLS-AA and one that comes from ATB, which produces GROMOS-compatible topologies. You're even trying to #include multiple force fields. This approach is fundamentally incorrect. You need to use one force field to describe all the components of your system.
-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.