Dear all, I am new to gromacs software. I was trying to make simple sodium nitrate (NaNO3) molecules. I have made .pdb file. then I got .gro file from pdb2gmx. But, I got struck in .itp file. Please help me. ( Na is nonbonded to any of N and O in NaNO3. And Na is also nonbonded to Na of 2nd NaNO3 molecule and so on). I have taken 50 NaNO3 molecules. Given below is .itp file, I cannot progress through grompp. as it is showing error as syntax error at '1 2 yes 1.0 1.0'. If possible correct my .itp file.
[ defaults ] ;nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ 1 2 yes 1.0 1.0 [ moleculetype ] ; molname nrexcl NaN 4 [ atomtypes ] ;name atnum mass charge ptype sigma epsilon Na 11 22.98977 1.000 A 3.33045e-01 1.15980e-02 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 O 8 15.99940 -0.598 A 2.86000e-01 8.78640e-01 N 7 14.00670 0.794 A 3.15000e-01 7.11280e-01 [ nonbond_params ] ;i j func sigma epsilonNa Na 1 3.33045e-01 3.33045e-01 Na O 1 3.33045e-01 1.15980e-02 Na N 1 3.33045e-01 1.15980e-02 [ constraints ] ; ai aj funct b0 [exclusions ] 1 2 1 3 1 4 1 5 Waiting for kind reply,Thank you, With Regards, SUMAIR FAISAL AHMED. -- 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.
