This probably is my ignorance but the error and the "bug" goes when I replaced CBX with NAC everywhere.
On Wed, Jul 7, 2010 at 4:47 PM, Justin A. Lemkul <[email protected]> wrote: > > > Sai Pooja wrote: > >> I checked again and the error does not go. Please read the steps below. >> >> The pdb file I started off with did not have any hydrogens. However, the >> way I had specified the capping residues in the .rtp file (SEE MARK'S MAIL), >> I had to specify hydrogens in the pdb file for the capping residues. So I >> used pymol to add hydrogens to my pdb file. I then used this file with >> charmm force field. However, pymol had added hydrogens everywhere and this >> was different from the definition of the standard residues defined in the >> .rtp file. I could not directly use -ignh because I needed the hydrogens for >> the capping residues. So I created a file that contained the hydrogens on >> the capping residues only. This resolved the error related to hydrogens. >> >> > Probably an easier and more reliable approach would simply be to create an > .hdb entry for your capping groups. > > > >> Error-from previous mail-NOT RESOLVED >> (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 >> >> > Maybe this is just showing up incorrectly in my mail client, but I wonder > if that CH3 is somehow misaligned and therefore not correctly identified. I > presume that you changed the residue name in the .rtp file accordingly? I > suppose the error message would be different (something like "residue not > found") but I just want to make sure. Mark's entry used NAC. > > > 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 ) >> >> The error stated in the previous mail(quoted above) occurred when I chose >> "none" for the both terminals or the carboxylic terminal option (using >> -ter). It worked fine if I chose "none" at the N terminal and any other >> option except "none" at the carboxylic acid terminal. So I chose "none" at N >> terminal and some option randomly at the carboxylic acid terminal. As >> expected, it adds a terminal at that end of the residue before my capping >> residue which is something I DONT want. I >> > > So does pdb2gmx somehow add the C-terminal cap after the carboxylate > terminus? > > > havent been able to find a way around it. Interestingly, when I generate a >> pdb file using -q, and open that pdb file in pymol, I dont get the terminal >> carboxylic acid that pdb2gmx gives in the .gro file. >> > > So the cap is applied properly in that structure? > > > I am not sure how to correct this. One way would be to remove those >> entries from the final .gro and .top file but not sure if that would be >> right. >> >> > This all sounds very fishy. This may be worth a bugzilla entry, but only > if you can build the structure in a very sound way, probably using .hdb > entries (or an appropriate all-atom structure, which you've yet to > demonstrate). > > -Justin > > Pooja >> >> >> >> >> >> >> >> On Sat, Jul 3, 2010 at 4:41 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> Sai Pooja wrote: >> >> Follow-up. It is easy to make it work. Just needed to be more >> rigorous. Thank you. >> >> >> It would be helpful if you describe what you mean. This error >> message is new to me, and appears to reflect new mechanics in the >> upcoming Gromacs release. If you describe what the problem was, how >> you resolved it, what your pdb2gmx command line was, and anything >> else that might be useful, that would likely help others solve this >> issue in the future. >> >> -Justin >> >> On Fri, Jul 2, 2010 at 5:43 PM, Sai Pooja <[email protected] >> <mailto:[email protected]> <mailto:[email protected] >> >> <mailto:[email protected]>>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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]> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>>> wrote: >> >> >> >> ----- Original Message ----- >> From: Sai Pooja <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected] >> >>>> >> Date: Friday, July 2, 2010 7:28 >> Subject: Re: [gmx-users] Capping residues >> To: [email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> <mailto:[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>>, >> Discussion list for >> GROMACS users <[email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>> <mailto:[email protected] >> >> <mailto:[email protected]> >> >> <mailto:[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]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> <mailto:[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]> >> <mailto:[email protected] >> <mailto:[email protected]>> >> <mailto:[email protected] >> <mailto:[email protected]> >> <mailto:[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 <http://vt.edu> <http://vt.edu> | >> >> (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list >> [email protected] <mailto:[email protected]> >> <mailto:[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]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> 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. >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- 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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