Follow-up. It is easy to make it work. Just needed to be more rigorous. Thank you.
On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <saipo...@gmail.com> wrote: > 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 <jalem...@vt.edu> 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 >>> <mark.abra...@anu.edu.au<mailto: >>> mark.abra...@anu.edu.au>> wrote: >>> >>> >>> >>> ----- Original Message ----- >>> From: Sai Pooja <saipo...@gmail.com <mailto:saipo...@gmail.com>> >>> Date: Friday, July 2, 2010 7:28 >>> Subject: Re: [gmx-users] Capping residues >>> To: jalem...@vt.edu <mailto:jalem...@vt.edu>, Discussion list for >>> GROMACS users <gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >>> >>> > 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 gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> >>> 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 gmx-users-requ...@gromacs.org >>> <mailto:gmx-users-requ...@gromacs.org>. >>> >>> 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 gmx-users@gromacs.org >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Quaerendo Invenietis-Seek and you shall discover. > -- Quaerendo Invenietis-Seek and you shall discover.
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