Dear Justin, I did as you said but I get the following error when I run grompp command. I don't know where is my mistake. What should I do to solve it?
Fatal error: Too many warnings (1), grompp terminated. If you are sure all warnings are harmless, use the -maxwarn option. Please see tables from the link: http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6-1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4 OH: the Zn-bound hydroxide oxygen atom when Zn-bound water is deprotonated, OW: Zn-bound water oxygen, NA and NB: the nitrogen atoms directly bound to the Zn +2 ion (NE2 (NB) atoms in His94 and His96, ND1 (NA) atom in His119). Table 1: specbond.dat: 14 HIS NA 1 ZN ZN 1 0.205 HISD ZNOH ;modified HIS NB 1 ZN ZN 1 0.205 HISE ZNOH ;modified ZN ZN 1 OH OH 1 0.18 ZNOH OH ;modified HIS NA 1 ZN ZN 1 0.205 HISD ZNOH2 ;modified HIS NB 1 ZN ZN 1 0.205 HISE ZNOH2 ;modified ZN ZN 1 OW OW 1 0.23 ZNOH2 HOH ;modified residuetypes.dat: ZNOH2 Ion ;modified ZNOH Ion ;modified Table 2: aminoacids.rtp: [ ZNOH];modified [ atoms ] ZN Zn 0.90920 1 [ ZNOH2 ];modified [ atoms ] ZN Zn 0.89230 1 Table 1: ffnonbonded.itp: OW 8 16.00 0.0000 A 1.76820e-01 6.371092e-01 ;modified Zn 30 65.4 0.0000 A 1.10000e-01 5.23250e-02 ;modified Table 1: ffbonded.itp: [ bondtypes ] ZN NA 1 0.20500 16744.00 ;modified ZN NB 1 0.20500 16744.00 ;modified ZN OH 1 0.18000 39348.40 ;modified ZN OW 1 0.23000 16744.00 ;modified [ angletypes ] C NA ZN 1 126.0 83.720 ;modified C NB ZN 1 126.0 83.720 ;modified NA ZN NB 1 109.5 96.278 ;modified NB ZN NB 1 109.5 96.278 ;modified NA ZN OH 1 109.5 96.278 ;modified NB ZN OH 1 109.5 96.278 ;modified ZN OH HW 1 124.0 83.720 ;modified HW OW HW 1 104.5 4186.0 ;modified [ dihedraltypes ] X ZN NA X 9 0.000 0.00000 3 ;modified X ZN NB X 9 0.000 0.00000 3 ;modified X ZN OH X 9 0.000 0.00000 3 ;modified X ZN OW X 9 0.000 0.00000 3 ;modified 2014-04-01 16:05 GMT+03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/1/14, 8:49 AM, Ahmet yıldırım wrote: > >> There are both Zn-OH(zinc-hydroxyl) and Zn-H2O (zinc-water) bond in >> structure, then should I modify "aminoacids.hdb" and "aminoacids.rtp" to >> add OH (hydroxyl) and water parameters? >> >> >> > The parameters listed in Table 1 need to be added to ffbonded.itp and > ffnonbonded.itp. The thing to watch out for is that there are two > different H-O-H angles that are defined, depending on whether the water is > free or bound to Zn. Therefore, you need unique atomtypes to differentiate > between different types of water, so that requires modification of > atomtypes.atp, as well, if you will be processing the structure with > pdb2gmx. > > Table 2 corresponds to a specific residue that needs to be added as an > .rtp entry (again, only if you are using pdb2gmx to create the topology). > The .hdb entry is only necessary if you do not have H positions in the > input coordinate file. > > -Justin > > > 2014-04-01 11:03 GMT+03:00 Ahmet yıldırım <ahmedo...@gmail.com>: >> >> Firstly, I will change ffnonbonded.itp and ffbonded.itp. Later? >>> >>> >>> 2014-04-01 10:37 GMT+03:00 Ahmet yıldırım <ahmedo...@gmail.com>: >>> >>> Dear users, >>> >>>> >>>> Please see the file from the link: >>>> >>>> http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source= >>>> web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F% >>>> 2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid% >>>> 3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei= >>>> DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6- >>>> 1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4 >>>> >>>> I want to add table 1 and table 2 parameters to amber force field. How >>>> can >>>> I achieve it? >>>> >>>> -- >>>> Ahmet Yıldırım >>>> >>>> >>> >>> >>> -- >>> Ahmet Yıldırım >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA 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. > -- Ahmet Yıldırım -- 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.