I used -ter option and selected "none" for both terminal ends but I still get this error:
Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS I have used Mark's definitions for capping residues in the rtp file. In the pdb file, this is what the capping residues look like: ATOM 33 N CBX 5 8.609 2.722 18.430 1.00 1.60 FR1 ATOM 34 H CBX 5 9.198 3.338 17.946 1.00 0.80 FR1 ATOM 35 CH3 CBX 5 7.176 2.594 17.895 1.00 2.17 FR1 ATOM 1 CH3 ACE 1 12.782 -0.027 28.022 1.00 2.17 FR1 ATOM 2 C ACE 1 12.532 -0.094 26.546 1.00 2.10 FR1 ATOM 3 O ACE 1 13.443 -0.213 25.696 1.00 1.60 FR1 On Fri, Jul 2, 2010 at 10:50 AM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > >> Thanks Marks. I tried it but this is what I get: >> >> Fatal error: >> atom N not found in buiding block 1ACE while combining tdb and rtp >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> >> Do I need to edit the aminoacids.n.tdb file as well? >> > > What are you choosing as your termini when running pdb2gmx? It should be > "none," since by capping, you are not choosing a protonation state for the > N- and C-termini. > > -Justin > > >> Pooja >> >> >> >> On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham >> <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> ----- Original Message ----- >> From: Sai Pooja <[email protected] <mailto:[email protected]>> >> Date: Friday, July 2, 2010 7:28 >> Subject: Re: [gmx-users] Capping residues >> To: [email protected] <mailto:[email protected]>, Discussion list for >> GROMACS users <[email protected] <mailto:[email protected]>> >> >> > I am sorry if I did not frame the question correctly, but putting >> it very simply, is there a way to use capping residues with the >> charmm forcefield if the residues are --COCH3 and NHCH3? >> >> Yes - you edit a copy of the .rtp file in your working directory and >> add whatever you want. Here's what I use in CHARMM >> >> [ ACE ] >> [ atoms ] >> CH3 CT3 -0.270 0 >> HH31 HA 0.090 0 >> HH32 HA 0.090 0 >> HH33 HA 0.090 0 >> C C 0.510 1 >> O O -0.510 1 >> [ bonds ] >> C CH3 >> C +N >> CH3 HH31 >> CH3 HH32 >> CH3 HH33 >> O C >> [ impropers ] >> C CH3 +N O >> >> [ NAC ] >> [ atoms ] >> N NH1 -0.470 1 >> HN H 0.310 1 >> CH3 CT3 -0.110 1 >> HH31 HA 0.090 1 >> HH32 HA 0.090 1 >> HH33 HA 0.090 1 >> [ bonds ] >> -C N >> N HN >> N CH3 >> CH3 HH31 >> CH3 HH32 >> CH3 HH33 >> >> [ impropers ] >> N -C CH3 HN >> -C CH3 N -O >> >> Mark >> -- >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected] >> <mailto:[email protected]>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Quaerendo Invenietis-Seek and you shall discover. >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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/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/mailing_lists/users.php > -- Quaerendo Invenietis-Seek and you shall discover.
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