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? Pooja On Thu, Jul 1, 2010 at 11:39 PM, Mark Abraham <[email protected]>wrote: > > > ----- Original Message ----- > From: Sai Pooja <[email protected]> > Date: Friday, July 2, 2010 7:28 > Subject: Re: [gmx-users] Capping residues > To: [email protected], Discussion list for GROMACS users < > [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] > 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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