Dear users, I renamed a water molecule' atoms bound to the Zn +2 ion in starting pdb. I get the following error by pdb2gmx (with -vsite hydrogens). How can I fix it? .. Making bonds... Number of bonds was 2, now 2 Warning: cannot convert atom 3 HZ1 (bound to a heavy atom OZ with 2 bonds and 2 bound hydrogens atoms) to virtual site
------------------------------------------------------- Program pdb2gmx, VERSION 4.5.5 HOH:OWZ O:OZ XXX.pdb: .. HETATM 2068 OZ OWZ A1001 -2.313 -0.628 16.011 1.00 8.54 O ... I modified as the following the some files. residuetypes.dat: OWZ water ;modified aminoacids.hdb: OWZ 1 ;modified 2 7 HZ OZ specbond.dat: ZN ZN 1 OWZ OZ 1 0.23 ZNOH2 ZOH2 ;modified aminoacids.rtp: [ OWZ ];modified [ atoms ] OZ OZ -0.8824 0 HZ1 HZ 0.5001 0 HZ2 HZ 0.5001 0 [ bonds ] OZ HZ1 OZ HZ2 atomtypes.atp: OZ 16.00000 ; modified HZ 1.00800 ; modified ffnonbonded.itp: OZ 8 16.00 0.0000 A 3.15061e-01 6.36386e-01 ;modified HZ 1 1.008 0.0000 A 0.00000e+00 0.00000e+00 ;modified 2014-04-02 16:35 GMT+03:00 Justin Lemkul <jalem...@vt.edu>: > > > On 4/2/14, 9:25 AM, Ahmet yıldırım wrote: > >> 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: >> >> > It's pointless for anyone to try to troubleshoot any of this without the > actual error produced by grompp. > > -Justin > > > 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=AFQjCNGUfMCQZYegoRpLGg5D9GjpFs >>>>>> PCxQ&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. >>> >>> >> >> >> > -- > ================================================== > > 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? 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