Dear Gromacs users, Please somebody help . editconf computs the incorrect value of "mass of input". I tried to resolve this problem but failed. Previously I was doing AOt but now I just found that the molecule OS1 =O2L showing error . Here I posted my A.pdb, RM.rtp atomtypes.atp. The mass of input should be 15.99940 but it showing 222. Please help me whether this is bug or something wrong with my GROMACS. Its GROMACS version 4.5.4. I tested for just 1 atom to see error
I have just 1 atom in my pdb so only on in .rtp too A.pdb CRYST1 12.000 12.000 12.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 OS1 AOT 151 7.820 -5.791 -0.815 1.00 0.00 O ENDMDL TER RM.rtp [ AOT ] ; [ atoms ] OS1 O2L -0.6000 1 [ bonds ] atomtypes.atp NTL 14.007000 ; ammonium nitrogen NH3L 14.007000 ; nitrogen phosphatidylethanolamine OBL 15.999400 ; acetic acid carboxyl oxygen (e. to protein OB) OCL 15.999400 ; acetate oxygen OSL 15.999400 ; ester oxygen OSLP 15.999400 ; Phosphate oxygen, to avoid conflict with methylacetate type O O2L 15.999400 ; Nucleic acid =O in phosphate or sulfate OHL 15.999400 ; Nucleic acid phosphate hydroxyl oxygen PL 30.974000 ; phosphorus SL 32.060000 ; Sulfate sulfur SOD 22.989770 ; Sodium Ion MG 24.305000 ; Magnesium Ion OUTPUT OF editconf Volume of input 125 (nm^3) Mass of input 222.295 (a.m.u.) This is incorrect, even to much incorrect. It should be 15.999940 Density of input 2.95304 (g/l) Scaling all box vectors by 0.143468 new system size : 0.000 0.000 0.000 shift : 2.141 2.141 2.141 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00 (nm^3) -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
