---------- Forwarded message ---------- From: Abhishek Agrawal <aintabhis...@gmail.com> Date: Tue, Mar 21, 2017 at 2:25 PM Subject: CNT Water and DNA protein, Not working To: gmx-us...@gromacs.org
Hare Krishna Everyone! OBJECITVE: See I am aiming to make a system having CNT Water DNA to study the interaction of DNA with the CNT, when CNT has some charged molecule attached to it or any one C be have some charge. SPECIFICATIONS: GROMACS 5.0.7 fftw Python VMD i3 5005 2.0 GHz 4GB Ubuntu 16.04 LTS PROBLEM: Going through many tutorials, gromacs mailing list and Andre tutorial for CNT on Gromacs site, I found that whatever I do, by making custom forcefield or going by default forcefield with the GROMACS nothing is working for me. It gives error that residue "UNL" or whatever the PDB has, is not found in the topolgy database,, this is for the default forcefield. I make custom one, then CNT is accepted but then on solvating the Water is not. Going forward DNA shall also be not accepted as it is not available in the custom forcefield. SUMMARY: What to do to make a system having: CNT Water and DNA, the FORCEFIELD is the major issue. Please guide. Regards, Abhishek Agrawal AMITY UNIVERSITY Research Associate @ NIT Patna NOIDA, INDIA -- 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.
