Dear Justin, You see, the ligand.itp contains the HS14 information as following,
.... 34 NT 1 ADP N6 7 -0.859 14.0067 35 HS14 1 ADP H10 7 0.406 1.0080 36 HS14 1 ADP H11 7 0.419 1.0080 .... But when I run gmx grompp -f ions.mdp -c target_solv.gro -p topol.top -o ions.tpr, it told me the "Atomtype HS14 not found". Will you please show me the way to have the issue settled? Brett At 2016-05-12 23:20:14, "Justin Lemkul" <jalem...@vt.edu> wrote: > > >On 5/12/16 11:17 AM, Brett wrote: >> Dear All, >> >> Following is the part of the atomtypes.atp for gromos54a7: >> >> O 15.99940 ; carbonyl oxygen (C=O) >> OM 15.99940 ; carboxyl oxygen (CO-) >> OA 15.99940 ; hydroxyl, sugar or ester oxygen >> OE 15.99940 ; ether or ester oxygen >> OW 15.99940 ; water oxygen >> N 14.00670 ; peptide nitrogen (N or NH) >> NT 14.00670 ; terminal nitrogen (NH2) >> NL 14.00670 ; terminal nitrogen (NH3) >> NR 14.00670 ; aromatic nitrogen >> NZ 14.00670 ; Arg NH (NH2) >> NE 14.00670 ; Arg NE (NH) >> C 12.01100 ; bare carbon >> CH0 12.0110 ; bare sp3 carbon, 4 bound heavy atoms >> CH1 13.01900 ; aliphatic or sugar CH-group >> CH2 14.02700 ; aliphatic or sugar CH2-group >> CH3 15.03500 ; aliphatic CH3-group >> CH4 16.04300 ; methane >> CH2r 14.02700 ; CH2-group in a ring >> ....... >> >> If I need to insert a new type list for example HS14 with weight 1.0080, >> should the word description of the atomtype (for example, "CH2-group in a >> ring" for "CH2r 14.02700") should be accurate or just a kind of reminder >> which the gromacas will not read? >> > >It's a comment; it's not used for anything. Note that atomtypes.atp is only >read by pdb2gmx, so if this is related to your earlier post (and if it is, >it's >better to continue a thread than to start a whole new topic) then you don't >need >to be editing this file. You need to be adding parameters in ffnonbonded.itp >or >the ligand's .itp file itself. > >> In addition, the atomtypes.atp is a readonly file in >> /usr/local/gromacs/share/gromacs/top/gromos54a7.ff/. WIll you please let me >> know how to save it after the HS14 atomtype was added? >> > >Make a local copy of the directory, acquire admin privileges, or (most simply) >add missing parameters into the ligand's .itp file. > >-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 | (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? 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.