OK, but when I chose none, it gives me a fatal error ( dangling bond! ). A new problem! So how do I solve it?
Sincerely, Shima ----- Original Message ----- From: Justin A. Lemkul <[email protected]> To: Discussion list for GROMACS users <[email protected]> Cc: Sent: Tuesday, June 26, 2012 8:09 PM Subject: Re: [gmx-users] H-atoms in .hdb file On 6/26/12 11:36 AM, Shima Arasteh wrote: > I tried again as below: > 1. defined FOR in .rtp file > 2. defined FOR in aminoacids.dat file. > 3. chose NH2 as N-Terminal > > and then got this topology for FOR and VAL: > ; residue 0 FOR rtp FOR q 0.0 > 1 CH1 0 FOR C 1 0.38 13.019 ; qtot >0.38 > 2 O 0 FOR O 1 -0.38 15.9994 ; qtot >0 > ; residue 1 VAL rtp VAL q 0.0 > 3 NL 1 VAL N 2 -0.83 14.0067 ; qtot >-0.83 > 4 H 1 VAL H1 2 0.415 1.008 ; qtot >-0.415 > 5 H 1 VAL H2 2 0.415 1.008 ; qtot >0 > 6 CH1 1 VAL CA 3 0 13.019 ; qtot >0 > 7 CH1 1 VAL CB 4 0 13.019 ; qtot >0 > 8 CH3 1 VAL CG1 5 0 15.035 ; qtot >0 > 9 CH3 1 VAL CG2 6 0 15.035 ; qtot >0 > 10 C 1 VAL C 7 0.38 12.011 ; qtot >0.38 > 11 O 1 VAL O 7 -0.38 15.9994 ; qtot >0 > > I guess the topology is correct. Isn't it? > > No, it isn't. An NH2 terminal says the N-terminus of VAL is a neutral amine. You should choose "None" for the terminus. The formyl group occupies the N-terminus as would another amino acid in a peptide bond, but there is no special protonation of FOR. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
