I think the corresponding dihedral (involving the HE2 atom) also need to be changed in the B state during the transformation.
On Thu, Jan 30, 2014 at 9:48 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/30/14, 11:12 AM, bipin singh wrote: > >> The protonated and deprotonated states will differ only in terms of >> presence or absence of hydrogens, thus in B state only that hydrogen atom >> which is intended to be transformed from protonated to deprotonated state >> will be altered in the terms of electrostatic and vdw parameters. >> >> > Incorrect. The atom types and charges for the whole carboxylate moiety > are affected by the removal of the proton. Only H becomes a dummy atom, > but the C and both O atoms of the resulting COO- group will be different > depending on protonation state. See GLU/GLUH in aminoacids.rtp. > > -Justin > > > >> On Thu, Jan 30, 2014 at 8:55 PM, Ozbil, Mehmet <m.oz...@umiami.edu> >> wrote: >> >> I see Bipin, >>> >>> Thanks. One quick question though, am I going to change the charges to >>> zero or all atoms to DUM atoms for all the atoms in B state or just for >>> the >>> hydrogen that will be transferred between the states (the atom where the >>> B >>> state was missing before): >>> >>> 16 opls_270 77 GLU HE2 5 0.45 1.008 >>> >>> Thanks again. >>> >>> Mehmet >>> >>> >>> ________________________________________ >>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin >>> singh <bipinel...@gmail.com> >>> Sent: Wednesday, January 29, 2014 10:46 PM >>> To: Discussion list for GROMACS users >>> Subject: Re: [gmx-users] free energy calculations for reference state for >>> constant pH MD simulations... >>> >>> You have to define the B state parameters for your deprotonated state >>> explicitly. >>> >>> The following line in your topology does not have the parameters for the >>> B >>> state. >>> >>> 16 opls_270 77 GLU HE2 5 0.45 1.008 >>> >>> You have to set the charges zero in the B state (if you want to consider >>> the change in electrostatic term only during deprotonation) or else >>> change >>> it to DUM atom (if you want to change both the vdw and electrostatics >>> terms >>> during deprotonation). >>> >>> >>> On Wed, Jan 29, 2014 at 8:15 PM, Ozbil, Mehmet <m.oz...@umiami.edu> >>> wrote: >>> >>> >>>> Thanks Bipin for the reply. >>>> >>>> I went through the Gromacs manual, and thought that I managed to >>>> incorporate two states (protonated and deprotonated) in my topology >>>> file. >>>> Can anyone who has done it before tell me if I defined both A and B >>>> >>> states >>> >>>> correctly in my .top file. >>>> >>>> ; >>>> ; File 'GLUA_prot_OPLS_p.top' was generated >>>> ; By user: onbekend (0) >>>> ; On host: onbekend >>>> ; At date: Tue Jan 28 13:49:17 2014 >>>> ; >>>> ; This is a standalone topology file >>>> ; >>>> ; It was generated using program: >>>> ; pdb2gmx - VERSION 4.5.4 >>>> ; >>>> ; Command line was: >>>> ; /home/apps/fas/Apps/Gromacs/gromacs-4.5.4-intel/bin//pdb2gmx -f >>>> GLUA_prot_OPLS.pdb -p GLUA_prot_OPLS_p.top -o GLUA_prot_OPLS_p.gro >>>> -inter >>>> ; >>>> ; Force field was read from the standard Gromacs share directory. >>>> ; >>>> >>>> ; Include forcefield parameters >>>> #include "oplsaa.ff/forcefield.itp" >>>> >>>> [ moleculetype ] >>>> ; Name nrexcl >>>> Protein_chain_A 3 >>>> >>>> [ atoms ] >>>> ; nr type resnr residue atom cgnr charge mass >>>> >>> typeB >>> >>>> chargeB massB >>>> ; residue 77 GLU rtp GLUH q 0.0 >>>> 1 opls_287 77 GLU N 1 -0.3 14.0067 >>>> opls_287 -0.3 14.0067 >>>> 2 opls_290 77 GLU H1 1 0.33 1.008 >>>> opls_290 0.33 1.008 >>>> 3 opls_290 77 GLU H2 1 0.33 1.008 >>>> opls_290 0.33 1.008 >>>> 4 opls_290 77 GLU H3 1 0.33 1.008 >>>> opls_290 0.33 1.008 >>>> 5 opls_299 77 GLU CA 1 0.15 12.011 >>>> opls_299 0.15 12.011 >>>> 6 opls_140 77 GLU HA 1 0.06 1.008 >>>> opls_140 0.06 1.008 >>>> 7 opls_136 77 GLU CB 2 -0.12 12.011 >>>> opls_136 -0.12 12.011 >>>> 8 opls_140 77 GLU HB1 2 0.06 1.008 >>>> opls_140 0.06 1.008 >>>> 9 opls_140 77 GLU HB2 2 0.06 1.008 >>>> opls_140 0.06 1.008 >>>> 10 opls_136 77 GLU CG 3 -0.12 12.011 >>>> opls_136 -0.12 12.011 >>>> 11 opls_140 77 GLU HG1 3 0.06 1.008 >>>> opls_140 0.06 1.008 >>>> 12 opls_140 77 GLU HG2 3 0.06 1.008 >>>> opls_140 0.06 1.008 >>>> 13 opls_267 77 GLU CD 4 0.52 12.011 >>>> opls_267 0.52 12.011 >>>> 14 opls_269 77 GLU OE1 4 -0.44 15.9994 >>>> opls_269 -0.44 15.9994 >>>> 15 opls_268 77 GLU OE2 5 -0.53 15.9994 >>>> opls_268 -0.53 15.9994 >>>> 16 opls_270 77 GLU HE2 5 0.45 1.008 >>>> 17 opls_271 77 GLU C 6 0.7 12.011 >>>> opls_271 0.7 12.011 >>>> 18 opls_272 77 GLU O1 6 -0.8 15.9994 >>>> opls_272 -0.8 15.9994 >>>> 19 opls_272 77 GLU O2 6 -0.8 15.9994 >>>> opls_272 -0.8 15.9994 >>>> >>>> [ bonds ] >>>> ; ai aj funct c0 c1 c2 >>>> c3 >>>> 1 2 1 >>>> 1 3 1 >>>> 1 4 1 >>>> 1 5 1 >>>> 5 6 1 >>>> 5 7 1 >>>> 5 17 1 >>>> 7 8 1 >>>> 7 9 1 >>>> 7 10 1 >>>> 10 11 1 >>>> 10 12 1 >>>> 10 13 1 >>>> 13 14 1 >>>> 13 15 1 >>>> 15 16 1 >>>> 17 18 1 >>>> 17 19 1 >>>> >>>> [ pairs ] >>>> ; ai aj funct c0 c1 c2 >>>> c3 >>>> 1 8 1 >>>> 1 9 1 >>>> 1 10 1 >>>> 1 18 1 >>>> 1 19 1 >>>> 2 6 1 >>>> 2 7 1 >>>> 2 17 1 >>>> 3 6 1 >>>> 3 7 1 >>>> 3 17 1 >>>> 4 6 1 >>>> 4 7 1 >>>> 4 17 1 >>>> 5 11 1 >>>> 5 12 1 >>>> 5 13 1 >>>> 6 8 1 >>>> 6 9 1 >>>> 6 10 1 >>>> 6 18 1 >>>> 6 19 1 >>>> 7 14 1 >>>> 7 15 1 >>>> 7 18 1 >>>> 7 19 1 >>>> 8 11 1 >>>> 8 12 1 >>>> 8 13 1 >>>> 8 17 1 >>>> 9 11 1 >>>> 9 12 1 >>>> 9 13 1 >>>> 9 17 1 >>>> 10 16 1 >>>> 10 17 1 >>>> 11 14 1 >>>> 11 15 1 >>>> 12 14 1 >>>> 12 15 1 >>>> 14 16 1 >>>> >>>> [ angles ] >>>> ; ai aj ak funct c0 c1 c2 >>>> c3 >>>> 2 1 3 1 >>>> 2 1 4 1 >>>> 2 1 5 1 >>>> 3 1 4 1 >>>> 3 1 5 1 >>>> 4 1 5 1 >>>> 1 5 6 1 >>>> 1 5 7 1 >>>> 1 5 17 1 >>>> 6 5 7 1 >>>> 6 5 17 1 >>>> 7 5 17 1 >>>> 5 7 8 1 >>>> 5 7 9 1 >>>> 5 7 10 1 >>>> 8 7 9 1 >>>> 8 7 10 1 >>>> 9 7 10 1 >>>> 7 10 11 1 >>>> 7 10 12 1 >>>> 7 10 13 1 >>>> 11 10 12 1 >>>> 11 10 13 1 >>>> 12 10 13 1 >>>> 10 13 14 1 >>>> 10 13 15 1 >>>> 14 13 15 1 >>>> 13 15 16 1 >>>> 5 17 18 1 >>>> 5 17 19 1 >>>> 18 17 19 1 >>>> >>>> [ dihedrals ] >>>> ; ai aj ak al funct c0 c1 c2 >>>> c3 c4 c5 >>>> 2 1 5 6 3 >>>> 2 1 5 7 3 >>>> 2 1 5 17 3 >>>> 3 1 5 6 3 >>>> 3 1 5 7 3 >>>> 3 1 5 17 3 >>>> 4 1 5 6 3 >>>> 4 1 5 7 3 >>>> 4 1 5 17 3 >>>> 1 5 7 10 3 dih_GLU_chi1_N_C_C_C >>>> 17 5 7 10 3 dih_GLU_chi1_C_C_C_CO >>>> 1 5 7 8 3 >>>> 1 5 7 9 3 >>>> 6 5 7 8 3 >>>> 6 5 7 9 3 >>>> 6 5 7 10 3 >>>> 17 5 7 8 3 >>>> 17 5 7 9 3 >>>> 1 5 17 18 3 >>>> 1 5 17 19 3 >>>> 6 5 17 18 3 >>>> 6 5 17 19 3 >>>> 7 5 17 18 3 >>>> 7 5 17 19 3 >>>> 5 7 10 11 3 >>>> 5 7 10 12 3 >>>> 5 7 10 13 3 >>>> 8 7 10 11 3 >>>> 8 7 10 12 3 >>>> 8 7 10 13 3 >>>> 9 7 10 11 3 >>>> 9 7 10 12 3 >>>> 9 7 10 13 3 >>>> 7 10 13 14 3 >>>> 7 10 13 15 3 >>>> 11 10 13 14 3 >>>> 11 10 13 15 3 >>>> 12 10 13 14 3 >>>> 12 10 13 15 3 >>>> 10 13 15 16 3 dih_sidechain_COOH_C_C_O_H >>>> 14 13 15 16 3 dih_sidechain_COOH_O_C_O_H >>>> >>>> [ dihedrals ] >>>> ; ai aj ak al funct c0 c1 c2 >>>> c3 >>>> 5 18 17 19 1 improper_O_C_X_Y >>>> 10 14 13 15 1 improper_O_C_X_Y >>>> >>>> ; Include Position restraint file >>>> #ifdef POSRES >>>> #include "posre.itp" >>>> #endif >>>> >>>> ; Include water topology >>>> #include "oplsaa.ff/tip3p.itp" >>>> >>>> #ifdef POSRES_WATER >>>> ; Position restraint for each water oxygen >>>> [ position_restraints ] >>>> ; i funct fcx fcy fcz >>>> 1 1 1000 1000 1000 >>>> #endif >>>> >>>> ; Include topology for ions >>>> #include "oplsaa.ff/ions.itp" >>>> >>>> [ system ] >>>> ; Name >>>> Protein in water >>>> >>>> [ molecules ] >>>> ; Compound #mols >>>> Protein_chain_A 1 >>>> SOL 4135 >>>> >>>> >>>> Thanks, >>>> Mehmet >>>> >>>> >>>> >>>> ________________________________________ >>>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < >>>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of bipin >>>> singh <bipinel...@gmail.com> >>>> Sent: Tuesday, January 28, 2014 2:46 AM >>>> To: Discussion list for GROMACS users >>>> Subject: Re: [gmx-users] free energy calculations for reference state >>>> for >>>> constant pH MD simulations... >>>> >>>> See the section "5.7.4 Topologies for free energy calculations" in >>>> >>> Gromacs >>> >>>> 4.6.5 manual. >>>> >>>> >>>> >>>> On Tue, Jan 28, 2014 at 3:09 AM, Ozbil, Mehmet <m.oz...@umiami.edu> >>>> >>> wrote: >>> >>>> >>>> Hello, >>>>> >>>>> I am trying to run constant pH MD with GROMACS, and started with the TI >>>>> free energy calculations. I am following Justin Lemkul`s free energy >>>>> calculation tutorial, and assuming that the free energy calculations >>>>> >>>> will >>> >>>> be similar to calculate the protonation energy of titratable amino >>>>> >>>> acids >>> >>>> such as GLU or HIS. >>>>> >>>>> My question is that, while scanning the lambda values for the free >>>>> >>>> energy >>> >>>> calculations do I need to define both protonated and deprotonated >>>>> >>>> states >>> >>>> of >>>> >>>>> GLU in the same .top and .pdb file, or I just use one .top and one .pdb >>>>> file and by changing the lambda values from 0.0 to 1.0 it does the >>>>> deprotonation itself. If I need to incorporate the two states in one >>>>> >>>> .top >>> >>>> and .pdb file can anyone help with how to do that? >>>>> >>>>> Thanks, >>>>> Mehmet Ozbil >>>>> -- >>>>> 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. >>>>> >>>>> >>>> >>>> >>>> -- >>>> >>>> >>>> >>>> *--------------------Thanks and Regards,Bipin Singh* >>>> -- >>>> 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? 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. >>>> >>>> >>> >>> >>> -- >>> >>> >>> >>> *--------------------Thanks and Regards,Bipin Singh* >>> -- >>> 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? 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. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > 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. > -- *--------------------Thanks and Regards,Bipin Singh* -- 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.