On 3/29/20 1:29 AM, Rolly Ng wrote:
Hello Justin, Thank you and yes. I went to the paper and it shows the steps for optimization. However, I have the following problems as I tried to follow the tutorial on CGenFF page, http://mackerell.umaryland.edu/~kenno/cgenff/download.php#tutor (1) what are these parameters in water_constr.inp? what values should I use in my case? if @stage eq 4 echo ######## USING MP2 GEOMETRY!!! ######## echo QM dipole (Debye) echo mp2/6-31g*: X= -3.1938 Y= 1.2595 Z= 0.0011 Tot= 3.4332 echo hf/6-31g*: X= -3.4411 Y= 1.3570 Z= 0.0012 Tot= 3.6990 (2) How can I get the correct value for the IC table for surface of interest? I suppose H2O molecules are placed one at a time to the C and N atoms of my molecule but where to place the dummy? generate dum first none last none setup warn noangle nodihedral join @residue dum renumber !preparation of IC table for surface of interest ic edit dihe 1 N2 1 C1 1 H1 3 dum 0.0 dihe 1 C1 1 H1 3 dum 4 dum 0.0 dihe 4 dum 3 dum 1 H1 2 oh2 180.0 end ic fill preserve ic edit dihe 3 dum 1 H1 2 oh2 2 h1 90.0 dihe 3 dum 1 H1 2 oh2 2 h2 -90.0 bond 1 H1 3 dum 1. bond 3 dum 4 dum 1. bond 1 H1 2 oh2 @d !varied bond 2 oh2 2 h1 0.9572 bond 2 oh2 2 h2 0.9572 angl 1 C1 1 H1 3 dum 90.0 angl 1 H1 3 dum 4 dum 90.0 angl 3 dum 1 H1 2 oh2 90.0 angl 1 H1 2 oh2 2 h1 127.74 angl 1 H1 2 oh2 2 h2 127.74 end How can I know the bond, angle and dihedral without a GUI show these parameters? Thanks for your patient.
If you have questions about CHARMM, you should use the CHARMM forum. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- 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.
