Hi, I am new to gromacs and I used acpype (amber2gromacs) tool to generate *.top and *.gro from Amber files *.prmtop and *.inpcrd. For water, this tool placed following in *.top file:
[ moleculetype ] ; molname nrexcl ; TIP3P model WAT 2 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 OW 1 WAT O 1 -0.834 16.00000 2 HW 1 WAT H1 1 0.417 1.00800 3 HW 1 WAT H2 1 0.417 1.00800 #ifdef FLEXIBLE [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 462750.4 1 3 1 0.09572 462750.4 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.520 836.800 #else [ settles ] ; i funct length-oh length -hh 1 1 0.09572 0.15139 [ exclusions ] 1 2 3 2 1 3 3 1 2 #endif [ system ] tio2_wpep [ molecules ] ; Compound nmols tio2_wpep 1 NA+ 1 WAT 3656 *My question is it does not include any topology details for 3656 water molecules either in this file or separately. Instead it has topology defined for standard water molecule in atoms section above. However, Gromacs accepted these two files as they are and runs were made. Please comment if I need to include water topology details for all 3656 water molecules. * Thanks Chetan -- 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.