On Apr 11, 2013 11:51 PM, "Laura Kingsley" <lking...@purdue.edu> wrote: > > So if I'm understanding you correctly in the .rtp file under > > [ HEME ] > [ dihedrals ] > > I should change: > HP42 CBD CGD O1D > HP42 CBD CGD O2D > ... > > to > > HP42 CBD CGD O1D 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000 > HP42 CBD CGD O2D 3 0.65270 1.95811 0.00000 -2.61082 0.00000 0.00000
I believe so. > > > Do I need to remove these definitions from the ffbonded.itp files then? Unused entries do no harm. Mark > > - Laura > > > > On 04/11/2013 05:43 PM, Mark Abraham wrote: >> >> On Thu, Apr 11, 2013 at 11:14 PM, Laura Kingsley<lking...@purdue.edu >wrote: >> >>> Hi Mark, >>> >>> We'd like to use the Ryckaert-Bellemans dihedral types. Does 3 not work in >>> the new version? >> >> >> Sorry, I was thinking of 4 and 9, which are basically interchangeable. The >> default for AMBER did change to 9 at some point (see top of >> aminoacids.rtp). You can use the old approach if you change the types of >> just the heme dihedrals to 3 in the .itp files produced by pdb2gmx. Or you >> can probably edit the heme .rtp entry to specify type 3 (plus parameters, >> perhaps via the #defines). >> >> Also, I took out the #define lines and replaced them with the actual >>> >>> atomtypes, because that didn't seem to work when I initially tried to add >>> just the #define lines to the ffbonded.itp file. >> >> >> The parameters need to go either on the lines in the .rtp that define the >> interactions, or on the lines that define the dihedraltypes. Only the >> latter needs the atom types (because that's how the lookup works). The >> old-style #defines cannot work in ffbonded.itp, because they assume the >> context of the .rtp, where the atoms are already identified. >> >> Mark >> >> >>> >>> On 04/11/2013 04:51 PM, Mark Abraham wrote: >>> >>>> Type 9 was added at some point to GROMACS to make coping with AMBER and >>>> CHARMM easier. So you should just change your #defines from 3 to 9. See >>>> table in chapter 5. Or you could just leave your solution in the same form >>>> as you did for the 4.0.x GROMACS. >>>> >>>> Mark >>>> >>>> >>>> On Thu, Apr 11, 2013 at 10:36 PM, Laura Kingsley<lking...@purdue.edu>** >>>> wrote: >>>> >>>> Hello Gromacs Users, >>>>> >>>>> >>>>> I am trying to update the contents of the top folder. I have parameters >>>>> for a HEME residue that worked in gromacs 4.0.7, and we're now trying to >>>>> update to gromacs 4.6.1 (long overdue), and need to migrate the >>>>> parameters >>>>> over to the new version. >>>>> >>>>> I have done the following: >>>>> >>>>> 1. added the HEME atomtypes to the atomtypes.atp file >>>>> 2. added the hydrogens to the aminoacids.hdb file >>>>> 3. added the [ HEME ] block to the aminoacids.rtp file >>>>> >>>>> >>>>> I am running into problems in adding the dihedrals. in the old version we >>>>> had used #define statements in the ffamber03bon.itp file (ffbonded.itp >>>>> in >>>>> the 4.6 version) , for example: >>>>> >>>>> #define heme_1 0.00000 0.00000 0.00000 0.00000 >>>>> 0.00000 0.00000 >>>>> #define heme_2 0.62760 1.88280 0.00000 -2.51040 >>>>> 0.00000 0.00000 >>>>> #define heme_3 0.65270 1.95811 0.00000 -2.61082 >>>>> 0.00000 0.00000 >>>>> #define heme_4 16.52680 0.00000 -16.52680 0.00000 >>>>> 0.00000 0.00000 >>>>> #define heme_5 62.76000 0.00000 -62.76000 0.00000 >>>>> 0.00000 0.00000 >>>>> >>>>> >>>>> the "heme_X" term was defined in the ffamber03.rtp file (aminoacids.rtp >>>>> file in ver 4.6)- for example: >>>>> >>>>> [ dihedrals ] >>>>> HP42 CBD CGD O1D heme_1 >>>>> HP42 CBD CGD O2D heme_1 >>>>> HP41 CBD CGD O1D heme_1 >>>>> HP41 CBD CGD O2D heme_1 >>>>> HP52 CAD CBD HP41 heme_2 >>>>> HP52 CAD CBD HP42 heme_2 >>>>> HP52 CAD CBD CGD heme_3 >>>>> >>>>> >>>>> >>>>> I updated all "define heme_X" lines in the ffbonded.itp file by going >>>>> back and putting in the actual atomtypes and the corresponding dihedral >>>>> function and parameters. For example: >>>>> >>>>> I replaced >>>>> #define heme_8 11.92440 0.00000 -11.92440 0.00000 >>>>> 0.00000 0.00000 >>>>> >>>>> with : >>>>> FE NO CC CD 3 11.92440 0.00000 -11.92440 0.00000 >>>>> 0.00000 0.00000 >>>>> >>>>> >>>>> >>>>> However, I'm getting errors from the grompp command about the dihedrals. >>>>> it gives: >>>>> >>>>> ERROR 1 [file prot_Other_chain_B2.itp, line 520]: >>>>> No default Proper Dih. types >>>>> >>>>> >>>>> ERROR 2 [file prot_Other_chain_B2.itp, line 521]: >>>>> No default Proper Dih. types >>>>> . >>>>> . >>>>> . >>>>> >>>>> >>>>> I'm thinking that it can't find the Dihedral types that I added t the >>>>> ffbonded.itp file, but I'm not sure why. One thing I've noticed is that >>>>> in >>>>> the .itp file generated by pdb2gmx the dihedral type for the heme is >>>>> given >>>>> as a 9, but in the ffbonded.itp file, I specify it as a 3. I'm not sure >>>>> where its reading this from. >>>>> >>>>> I'm hoping that this is just a simple thing that I'm missing and someone >>>>> can help point me in the right direction. >>>>> >>>>> >>>>> Thanks, >>>>> >>>>> - Laura >>>>> >>>>> >>>>> >>>>> -- >>>>> Laura Kingsley >>>>> >>>>> Graduate Student >>>>> Medicinal Chemistry and Molecular Pharmacology >>>>> Purdue University >>>>> Office: RHPH 504A >>>>> 575 Stadium Mall Dr. >>>>> West Lafayette, IN 47907 >>>>> Office Phone: (765) 496-6643 >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users< http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users< http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> >>>>> * Please search the archive at http://www.gromacs.org/** >>>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>>> >>>>> Mailing_Lists/Search< 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< http://www.gromacs.org/**Support/Mailing_Lists> >>>>> <http://**www.gromacs.org/Support/**Mailing_Lists< http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>> -- >>> Laura Kingsley >>> >>> Graduate Student >>> Medicinal Chemistry and Molecular Pharmacology >>> Purdue University >>> Office: RHPH 504A >>> 575 Stadium Mall Dr. >>> West Lafayette, IN 47907 >>> Office Phone: (765) 496-6643 >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/**mailman/listinfo/gmx-users< http://lists.gromacs.org/mailman/listinfo/gmx-users> >>> * Please search the archive at http://www.gromacs.org/** >>> Support/Mailing_Lists/Search< 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< http://www.gromacs.org/Support/Mailing_Lists> >>> > > -- > Laura Kingsley > > Graduate Student > Medicinal Chemistry and Molecular Pharmacology > Purdue University > Office: RHPH 504A > 575 Stadium Mall Dr. > West Lafayette, IN 47907 > Office Phone: (765) 496-6643 > > -- > 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 -- 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