I will answer my own question: I found in another post that indeed in GROMACS its Rmin.
Thanks > On Sep 25, 2015, at 5:25 PM, Ebert Maximilian <m.eb...@umontreal.ca> wrote: > > Yeah that is what I thought but that’s life. > > One more question.In the [ atomtypes ] section I need the sigma and epsilon > value. In found them in the GAFF FF in the MOD4 section. In GROMACS sigma is > in nm and epsilon in KJ/mol. In GAFF epsilon is in Kcal/mol and sigma is in > angstroem and defined as r0 which is sigma *( the 6th root of 2). > > So I picked an atomtype which is defined in the same way in AMBER and GAFF to > see if I am doing the conversion right. A standard carbon CA is similar in > both since the definition is taken from OPLS: > > GAFF ca r0: 1.9080 epsilon: 0.0860 > > If I look in the AMBER FF in GROMACS this changes to > > AMBER FF in GROMACS CA sigma: 3.39967e-01 epsilon: 3.59824e-01 > > If I convert now the 0.086 kcal/mol into kj/mol I get 3.59824e-01 which is as > expected. However, for sigma I get only 1.6998e-01 instead of 3.39967e-01, > which is half. Why is the sigma value in GROMACS two times the sigma value in > GAFF? Is GAFF using Rmin/2 and GROMACS Rmin? It seems like it but I just > wanted to be sure. > > Thanks > >> On Sep 25, 2015, at 4:43 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> >> On 9/25/15 4:40 PM, Ebert Maximilian wrote: >>> I read that and this is the way I added the cysteine to AMBER which >>> connects to the heme. Now I am adding the heme but the FF definition for >>> bonds, angles, etc are all in lower case for the GAFF FF. From you answer I >>> guess I need to add these lower case atom types and the bonds, angles, etc >>> definition from the GAFF FF to the AMBER FF manually. >>> >> >> Indeed, which is what steps 3 and 4 tell you. Adding a residue is simple, >> but if that residue involves modifications to the force field, then there is >> more work to be done. >> >> -Justin >> >>> Not much fun but I will share the work here in the end. Maybe this will >>> help people who want to simulate heme containing proteins in GROMACS and >>> AMBER99SB-ILDN. >>> >>> Have a good weekend, >>> Max >>> >>> >>> On Sep 25, 2015, at 4:25 PM, Justin Lemkul >>> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >>> >>> >>> >>> On 9/25/15 4:22 PM, Ebert Maximilian wrote: >>> Since the heme definition in AMBER uses GAFF atom types how do I get the >>> GAFF FF to work in GROMACS? I would need all the bonded and non bonded >>> definitions of GAFF for the heme in der AMBER FF port in GROMACS right? >>> >>> >>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field >>> >>> -Justin >>> >>> Max >>> >>> On Sep 25, 2015, at 1:36 PM, Justin Lemkul >>> <jalem...@vt.edu<mailto:jalem...@vt.edu>> wrote: >>> >>> >>> >>> On 9/25/15 1:32 PM, Ebert Maximilian wrote: >>> Hi there, >>> >>> I am trying to simulate a heme containing protein. I found AMBER heme >>> parameters in the mol2 and frcmod file format. I know that I can generate >>> .itp files containing the parameters, which I can later add to my .top file. >>> However, it would be much easier to use pdb2gmx directly without stripping >>> the heme and the cysteine binding the heme and later manually add it again. >>> I >>> added the cysteine to the standard amber force field. However, before adding >>> the heme manually I wanted to know if there is a way to load an itp file >>> while executing pdb2gmx? >>> >>> >>> pdb2gmx does not need .itp information. grompp does. Add the parameters >>> to ffbonded.itp or ffnonbonded.itp as needed. >>> >>> How would you add the information from the cysteine in mol2 format and the >>> heme in mol2/frcmod format to amber in gromacs? >>> >>> >>> Charges and connectivity go in the .rtp entry. Heme ligation by His and >>> Cys is already supported via specbond.dat. >>> >>> -Justin >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu<mailto:jalem...@outerbanks.umaryland.edu> >>> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to gmx-users-requ...@gromacs.org. >>> >>> >>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu<mailto:jalem...@outerbanks.umaryland.edu> >>> | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >>> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >>> * For (un)subscribe requests visit >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send >>> a mail to >>> gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. >>> >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a >> mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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