Hi Mark,
Thank you for your reply. But, I couldn’t understand very well what you meant “you can make one that uses backbone-style linking. Most of the forcefields will have examples of non-amino-acid terminating residues - these make a single peptide bond just like yours does.”. So, let me explain the problem a little more. I would be happy if you could expound upon your reply. *1)* I prepared the *rtp *entry for the lauroic acid (see below) and add the lipid parameters to the relevant sections of the *ffnonbonded.itp*and *ffbonded.itp* files. *2)* I added the lauroic acid as a "Non-Protein” in the * residuetypes.dat *file and also I introduced the atom types (LO: 15.9994, LC: 12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.* *3) *I concatenated the structure files of a 8-residue-peptide* *and lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained the *topol.top, conf.gro* and *posre.itp* for *the whole system.* (I chose : start terminus VAL-2: NH2 and end terminus ASP-9: COO-) *4)* But when I looked into *conf.gro* with the VMD, I see that the peptide bond is formed between the lauroic acid (C34) and the N terminal of the Valine. However, second H of the N is still there and it is making another bond with C34 of lauroic acid. The strange thing is: C34 is double bonded to O35, Carbon makes four bonds. How can I get rid of that H? [ DPP ] [ atoms ] C34 LC 0.800 18 O35 LO -0.60 18 C36 LP2 0 19 C37 LP2 0 20 C38 LP2 0 21 C39 LP2 0 22 C40 LP2 0 23 C41 LP2 0 24 C42 LP2 0 25 C43 LP2 0 26 C44 LP2 0 27 C45 LP2 0 28 C46 LP3 0 29 [ bonds ] ; ai aj funct 34 35 1 0.12300E+00 0.50210E+06 34 36 1 0.15300E+00 0.33470E+06 36 37 1 0.15300E+00 0.33470E+06 37 38 1 0.15300E+00 0.33470E+06 38 39 1 0.15300E+00 0.33470E+06 39 40 1 0.15300E+00 0.33470E+06 40 41 1 0.15300E+00 0.33470E+06 41 42 1 0.15300E+00 0.33470E+06 42 43 1 0.15300E+00 0.33470E+06 43 44 1 0.15300E+00 0.33470E+06 44 45 1 0.15300E+00 0.33470E+06 45 46 1 0.15300E+00 0.33470E+06 [ angles ] ; ai aj ak funct 34 36 37 1 0.11100E+03 0.46020E+03 35 34 36 1 0.12100E+03 0.50210E+03 36 37 38 1 0.11100E+03 0.46020E+03 37 38 39 1 0.11100E+03 0.46020E+03 38 39 40 1 0.11100E+03 0.46020E+03 39 40 41 1 0.11100E+03 0.46020E+03 40 41 42 1 0.11100E+03 0.46020E+03 41 42 43 1 0.11100E+03 0.46020E+03 42 43 44 1 0.11100E+03 0.46020E+03 43 44 45 1 0.11100E+03 0.46020E+03 44 45 46 1 0.11100E+03 0.46020E+03 [ dihedrals ] ; ai aj ak al funct phi0 cp mult 34 36 37 38 1 0.0 5.86 3 36 37 38 39 3 37 38 39 40 3 38 39 40 41 3 39 40 41 42 3 40 41 42 43 3 41 42 43 44 3 42 43 44 45 3 43 44 45 46 3 Best regards, Deniz On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote: > >> >> Hi Gromacs users, >> >> I want to covalently link the lauroic acid to the Valine residue (it is a >> peptide (amide) bond), I know that I should update the specbond.dat.But >> before updating this file, I need the NH as an N terminal of the first >> residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3, >> NH2 or None instead of NH.So, I add the [NH] directive in the >> aminoacids.n.rtp file, as follows; >> >> >> [ NH ] >> >> [ replace ] >> >> ; old-namenew-typenew-massnew-charge >> >> NLN14.0067-0.31 >> >> CACH113.0190.127 >> >> [ add ] >> >> 12HNCAC >> >> ;atom_typemasscharge >> >> H1.0080.31 >> >> [ delete ] >> >> H >> >> [ bonds ] >> >> NHgb_2 >> >> [ angles ] >> >> CANHga_11 >> >> [ dihedrals ] >> >> HNCACgd_29 >> >> >> >> (ps. I wrote the charges of N, CA and H according to values defined in >> topol.top and also I used the Gromos96 53a6 force field) >> >> >> Then, I used the pdb2gmx with –ter, I could see: >> >> Select start terminus type for VAL >> >> 0: NH >> >> 1: NH3+ >> >> 2: NH2 >> >> 3: None >> >> >> Finally, I got thetopol.top, posre itp and conf.gro files. But when I >> looked into conf.gro, I see that I am getting “None”. How can I get the NH ? >> >> > Coordinating multiple "moving parts" like the specbond and terminus-fixing > is probably a recipe for trouble. > > Since you have to make an .rtp entry for lauroic acid anyway, you can make > one that uses backbone-style linking. Most of the forcefields will have > examples of non-amino-acid terminating residues - these make a single > peptide bond just like yours does. Now you can ignore the specbond and > terminus-fixing mechanisms entirely. > > Mark > -- > 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 >
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