Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file
On 5/26/19 9:13 AM, Lalehan Ozalp wrote: Thank you Justin, I worked more on the format of hydrogen names and I don't see those errors anymore. However, the only error I now see is: "Atom H5'1 not found in rtp database in residue FAD, it looks a bit like H01". Which is weird, because there is no atom named H5'1 anywhere! Not in the pdb, not in the rtp, not itp nor hdb file. This is absolutely a black box to me. Your force field has an .arn (atom renaming) file that is translating H5' to H5'1 and therefore looking for H5'1 in the coordinate file. It's not finding it (probably because your .rtp specifies H5' and so does your .hdb). -Justin Thanks again! On Thu, May 23, 2019 at 12:07 AM Justin Lemkul wrote: On 5/22/19 4:14 PM, Lalehan Ozalp wrote: Hello all, I am trying to run a simulation with a protein involving a covalently bound FAD cofactor. I followed the steps provided on the website http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and -I think- added the hydrogens in the .hdb file accordingly. While doing this, I specifically used the atom types that gromacs would recognize (I also added relevant .rtp and .itp file to the forcefield in the current working directory). However, several warnings and subsequently a fatal error occurs when I run pdb2gmx. I don't prefer using -missing option in this case as it'll probably give a wrong topology. How to come around this? Any help would be appreciated. I provide the warnings and the error message below; as well as the constitution of the hydrogens in the .hdb file: (.hdb file) FAD 6 2 3 H N2CA NC 3 4 HC CT CA CA 1 1 HC CA CA CT 1 1 H5 CQ NC CA 1 1 H5 CQ NA CT 1 1 HA CA CA CT This entry cannot be correct, because the same atoms are defined in multiple ways. Note that the .hdb file requires atom *names*, not types. The errors listed below indicated you have 30 more hydrogens that are unaccounted for. FAD is a big molecule, you have to include all the hydrogens in the isoalloxazine, adenosine, and ribitol. -Justin WARNING: atom H01 is missing in residue FAD 600 in the pdb file You might need to add atom H01 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H02 is missing in residue FAD 600 in the pdb file You might need to add atom H02 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H03 is missing in residue FAD 600 in the pdb file You might need to add atom H03 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H04H is missing in residue FAD 600 in the pdb file You might need to add atom H04H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H05 is missing in residue FAD 600 in the pdb file You might need to add atom H05 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H06H is missing in residue FAD 600 in the pdb file You might need to add atom H06H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H07 is missing in residue FAD 600 in the pdb file You might need to add atom H07 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H08H is missing in residue FAD 600 in the pdb file You might need to add atom H08H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H09 is missing in residue FAD 600 in the pdb file You might need to add atom H09 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H10 is missing in residue FAD 600 in the pdb file You might need to add atom H10 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H11 is missing in residue FAD 600 in the pdb file You might need to add atom H11 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H12 is missing in residue FAD 600 in the pdb file You might need to add atom H12 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H13 is missing in residue FAD 600 in the pdb file You might need to add atom H13 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H14 is missing in residue FAD 600 in the pdb file You might need to add atom H14 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H15 is missing in residue FAD 600 in the pdb file
Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file
Thank you Justin, I worked more on the format of hydrogen names and I don't see those errors anymore. However, the only error I now see is: "Atom H5'1 not found in rtp database in residue FAD, it looks a bit like H01". Which is weird, because there is no atom named H5'1 anywhere! Not in the pdb, not in the rtp, not itp nor hdb file. This is absolutely a black box to me. Thanks again! On Thu, May 23, 2019 at 12:07 AM Justin Lemkul wrote: > > > On 5/22/19 4:14 PM, Lalehan Ozalp wrote: > > Hello all, > > > > I am trying to run a simulation with a protein involving a covalently > bound > > FAD cofactor. I followed the steps provided on the website > > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > and -I think- added the hydrogens in the .hdb file accordingly. While > doing > > this, I specifically used the atom types that gromacs would recognize (I > > also added relevant .rtp and .itp file to the forcefield in the current > > working directory). > > > > However, several warnings and subsequently a fatal error occurs when I > run > > pdb2gmx. I don't prefer using -missing option in this case as it'll > > probably give a wrong topology. > > > > How to come around this? Any help would be appreciated. I provide the > > warnings and the error message below; as well as the constitution of the > > hydrogens in the .hdb file: > > (.hdb file) > > FAD 6 > > 2 3 H N2CA NC > > 3 4 HC CT CA CA > > 1 1 HC CA CA CT > > 1 1 H5 CQ NC CA > > 1 1 H5 CQ NA CT > > 1 1 HA CA CA CT > > > > This entry cannot be correct, because the same atoms are defined in > multiple ways. Note that the .hdb file requires atom *names*, not types. > The errors listed below indicated you have 30 more hydrogens that are > unaccounted for. FAD is a big molecule, you have to include all the > hydrogens in the isoalloxazine, adenosine, and ribitol. > > -Justin > > > WARNING: atom H01 is missing in residue FAD 600 in the pdb file > > You might need to add atom H01 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H02 is missing in residue FAD 600 in the pdb file > > You might need to add atom H02 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H03 is missing in residue FAD 600 in the pdb file > > You might need to add atom H03 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H04H is missing in residue FAD 600 in the pdb file > > You might need to add atom H04H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H05 is missing in residue FAD 600 in the pdb file > > You might need to add atom H05 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H06H is missing in residue FAD 600 in the pdb file > > You might need to add atom H06H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H07 is missing in residue FAD 600 in the pdb file > > You might need to add atom H07 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H08H is missing in residue FAD 600 in the pdb file > > You might need to add atom H08H to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H09 is missing in residue FAD 600 in the pdb file > > You might need to add atom H09 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H10 is missing in residue FAD 600 in the pdb file > > You might need to add atom H10 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H11 is missing in residue FAD 600 in the pdb file > > You might need to add atom H11 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H12 is missing in residue FAD 600 in the pdb file > > You might need to add atom H12 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H13 is missing in residue FAD 600 in the pdb file > > You might need to add atom H13 to the hydrogen database of > > building block FAD > > in the file FAD.hdb (see the manual) > > > > > > WARNING: atom H14 is missing in residue FAD 600 in the pdb file > > You might need to add atom H14 to the hydrogen database of > > building block FAD > > in the file
Re: [gmx-users] error of missing atoms due to an incorrectness in the .hdb file
On 5/22/19 4:14 PM, Lalehan Ozalp wrote: Hello all, I am trying to run a simulation with a protein involving a covalently bound FAD cofactor. I followed the steps provided on the website http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and -I think- added the hydrogens in the .hdb file accordingly. While doing this, I specifically used the atom types that gromacs would recognize (I also added relevant .rtp and .itp file to the forcefield in the current working directory). However, several warnings and subsequently a fatal error occurs when I run pdb2gmx. I don't prefer using -missing option in this case as it'll probably give a wrong topology. How to come around this? Any help would be appreciated. I provide the warnings and the error message below; as well as the constitution of the hydrogens in the .hdb file: (.hdb file) FAD 6 2 3 H N2CA NC 3 4 HC CT CA CA 1 1 HC CA CA CT 1 1 H5 CQ NC CA 1 1 H5 CQ NA CT 1 1 HA CA CA CT This entry cannot be correct, because the same atoms are defined in multiple ways. Note that the .hdb file requires atom *names*, not types. The errors listed below indicated you have 30 more hydrogens that are unaccounted for. FAD is a big molecule, you have to include all the hydrogens in the isoalloxazine, adenosine, and ribitol. -Justin WARNING: atom H01 is missing in residue FAD 600 in the pdb file You might need to add atom H01 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H02 is missing in residue FAD 600 in the pdb file You might need to add atom H02 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H03 is missing in residue FAD 600 in the pdb file You might need to add atom H03 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H04H is missing in residue FAD 600 in the pdb file You might need to add atom H04H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H05 is missing in residue FAD 600 in the pdb file You might need to add atom H05 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H06H is missing in residue FAD 600 in the pdb file You might need to add atom H06H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H07 is missing in residue FAD 600 in the pdb file You might need to add atom H07 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H08H is missing in residue FAD 600 in the pdb file You might need to add atom H08H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H09 is missing in residue FAD 600 in the pdb file You might need to add atom H09 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H10 is missing in residue FAD 600 in the pdb file You might need to add atom H10 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H11 is missing in residue FAD 600 in the pdb file You might need to add atom H11 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H12 is missing in residue FAD 600 in the pdb file You might need to add atom H12 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H13 is missing in residue FAD 600 in the pdb file You might need to add atom H13 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H14 is missing in residue FAD 600 in the pdb file You might need to add atom H14 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H15 is missing in residue FAD 600 in the pdb file You might need to add atom H15 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H16 is missing in residue FAD 600 in the pdb file You might need to add atom H16 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H17 is missing in residue FAD 600 in the pdb file You might need to add atom H17 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H18 is missing in residue FAD 600 in the pdb file You might need to add atom H18 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H19 is missing in
[gmx-users] error of missing atoms due to an incorrectness in the .hdb file
Hello all, I am trying to run a simulation with a protein involving a covalently bound FAD cofactor. I followed the steps provided on the website http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field and -I think- added the hydrogens in the .hdb file accordingly. While doing this, I specifically used the atom types that gromacs would recognize (I also added relevant .rtp and .itp file to the forcefield in the current working directory). However, several warnings and subsequently a fatal error occurs when I run pdb2gmx. I don't prefer using -missing option in this case as it'll probably give a wrong topology. How to come around this? Any help would be appreciated. I provide the warnings and the error message below; as well as the constitution of the hydrogens in the .hdb file: (.hdb file) FAD 6 2 3 H N2CA NC 3 4 HC CT CA CA 1 1 HC CA CA CT 1 1 H5 CQ NC CA 1 1 H5 CQ NA CT 1 1 HA CA CA CT WARNING: atom H01 is missing in residue FAD 600 in the pdb file You might need to add atom H01 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H02 is missing in residue FAD 600 in the pdb file You might need to add atom H02 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H03 is missing in residue FAD 600 in the pdb file You might need to add atom H03 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H04H is missing in residue FAD 600 in the pdb file You might need to add atom H04H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H05 is missing in residue FAD 600 in the pdb file You might need to add atom H05 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H06H is missing in residue FAD 600 in the pdb file You might need to add atom H06H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H07 is missing in residue FAD 600 in the pdb file You might need to add atom H07 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H08H is missing in residue FAD 600 in the pdb file You might need to add atom H08H to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H09 is missing in residue FAD 600 in the pdb file You might need to add atom H09 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H10 is missing in residue FAD 600 in the pdb file You might need to add atom H10 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H11 is missing in residue FAD 600 in the pdb file You might need to add atom H11 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H12 is missing in residue FAD 600 in the pdb file You might need to add atom H12 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H13 is missing in residue FAD 600 in the pdb file You might need to add atom H13 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H14 is missing in residue FAD 600 in the pdb file You might need to add atom H14 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H15 is missing in residue FAD 600 in the pdb file You might need to add atom H15 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H16 is missing in residue FAD 600 in the pdb file You might need to add atom H16 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H17 is missing in residue FAD 600 in the pdb file You might need to add atom H17 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H18 is missing in residue FAD 600 in the pdb file You might need to add atom H18 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H19 is missing in residue FAD 600 in the pdb file You might need to add atom H19 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H21 is missing in residue FAD 600 in the pdb file You might need to add atom H21 to the hydrogen database of building block FAD in the file FAD.hdb (see the manual) WARNING: atom H22 is missing in residue FAD 600 in the pdb file
