Hi You can see that only the problem is coming from hydrogen. So in pdb2gmx command use -ignh so that it ignores the hydrogen. If you use this this WARNING will not come.
On Fri, Aug 24, 2018 at 4:00 AM, Amir Zeb <zebami...@gmail.com> wrote: > Thanks Justin, > > Actually I used Parachem CGenFF server https://cgenff.umaryland.edu/ and > generated the parameters for KAC. > The merged.rtp file was modified by adding the KAC parameters > That issue fixed, but now I'm getting the following warning which > ultimately results in fatal error. > > WARNING: atom HA is missing in residue KAC 33 in the pdb file > You might need to add atom HA to the hydrogen database of building > block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HB1 is missing in residue KAC 33 in the pdb file > You might need to add atom HB1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HB2 is missing in residue KAC 33 in the pdb file > You might need to add atom HB2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HG1 is missing in residue KAC 33 in the pdb file > You might need to add atom HG1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HG2 is missing in residue KAC 33 in the pdb file > You might need to add atom HG2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HD1 is missing in residue KAC 33 in the pdb file > You might need to add atom HD1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HD2 is missing in residue KAC 33 in the pdb file > You might need to add atom HD2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HE1 is missing in residue KAC 33 in the pdb file > You might need to add atom HE1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HE2 is missing in residue KAC 33 in the pdb file > You might need to add atom HE2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HZ1 is missing in residue KAC 33 in the pdb file > You might need to add atom HZ1 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI11 is missing in residue KAC 33 in the pdb file > You might need to add atom HI11 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI12 is missing in residue KAC 33 in the pdb file > You might need to add atom HI12 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HI13 is missing in residue KAC 33 in the pdb file > You might need to add atom HI13 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HZ2 is missing in residue KAC 33 in the pdb file > You might need to add atom HZ2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > > WARNING: atom HT2 is missing in residue KAC 33 in the pdb file > You might need to add atom HT2 to the hydrogen database of > building block KAC > in the file merged.hdb (see the manual) > > How may I fix this issue? > > Thanks in advance! > > > On Wed, Aug 22, 2018 at 4:31 AM Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 8/22/18 5:26 AM, Bratin Kumar Das wrote: > > > Hi > > > In your tool.top file the particular lys molecule residue name you > > have > > > to modify. Then it will work..Actually grompp can't find the molecule > in > > > the topology. > > > > The error has nothing to do with grompp. The topology was never created > > because pdb2gmx could not write a topology for KAC. > > > > CHARMM36 does support KAC, but not as a standalone residue. In CHARMM, > > one would generate a normal lysine then patch it with the KAC patch. To > > make this work in GROMACS, one would have to create a KAC .rtp entry by > > applying the same logic - modify LYS according to the KAC patch (found > > in the stream/prot/toppar_all36_prot_modify_res.str file from the > > tarball distributed by Alex MacKerell: > > http://mackerell.umaryland.edu/charmm_ff.shtml#charmm). > > > > -Justin > > > > > On Wed 22 Aug, 2018, 2:53 PM Bratin Kumar Das, < > > 177cy500.bra...@nitk.edu.in> > > > wrote: > > > > > >> Hi > > >> In your tool.top file the particular lys molecule residue name > you > > >> have to modify. Then it will work..Actually grompp can't find the > > molecule > > >> in the topology. > > >> > > >> On Wed 22 Aug, 2018, 11:35 AM Amir Zeb, <zebami...@gmail.com> wrote: > > >> > > >>> Hi gromacs users, > > >>> > > >>> I want to simulate a protein where one of the lysine residues is > > modified > > >>> to acetylated lysine and has been denoted by KAC. I want to simulate > > it by > > >>> CharmM 36 ff, but it gave me this error. > > >>> > > >>> > > >>> Program gmx pdb2gmx, VERSION 5.1.4 > > >>> Source code file: > > >>> /home/chip/Downloads/gromacs-5.1.4/src/gromacs/ > gmxpreprocess/resall.c, > > >>> line: 645 > > >>> > > >>> Fatal error: > > >>> Residue 'KAC' not found in residue topology database > > >>> For more information and tips for troubleshooting, please check the > > >>> GROMACS > > >>> website at http://www.gromacs.org/Documentation/Errors > > >>> > > >>> > > >>> Is CharmM 36 ff capable to simulate modified residue acetylated > lysine? > > >>> If yes, what is the ff compatible notation for acetylated lysine? > > >>> If not, which ff can I use to simulate acetylated lysine? > > >>> > > >>> Thanks in advance! > > >>> > > >>> Amir > > >>> -- > > >>> 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. > > Assistant Professor > > Virginia Tech Department of Biochemistry > > > > 303 Engel Hall > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > 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. > -- 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.