In fact the genion does not add the neutralizing CL ions to gro file! Why? How can I solve this problem?
Would you please help me? Sincerely, Shima ----- Original Message ----- From: Shima Arasteh <shima_arasteh2...@yahoo.com> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Cc: Sent: Sunday, March 24, 2013 5:16 PM Subject: gro does not match top Hi, I am solving a protein in water. This protein has a charge of +3. After solvation there is 3272 water molecules. Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system. #genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1 After this, the top file shows: Protein_chain_A 1 SOL 3147 NA 61 CL 61 CL 3 But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error. What' s your suggestions? How does it come? Thanks in advance. Sincerely, Shima -- 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
