Hello fellow GROMACS users,<br><br>I am in the process of constructing a new residue in the OPLS-AA force field for the mCherry chromophore. However, I am having some difficulty in adding three CH3 hydrogens. In the 2H5Q PDB structure the chromophore residue, CH6, has CE1 and CE2 ring carbons defined, but also an extended chain carbon named CE. The problem is that my hdb rules were assigning HE1 and HE2 to the ring carbon hydrogens (1 1 HE1 CE1 CD1 CZ for example), and HE1, HE2, and HE3 to the CE carbon hydrogens (3 4 HE CE SD CG1). Since these hydrogens are of different types, I need to have them named distinctly in my RTP file and need for Gromacs to understand them as different types. I changed the CH6 residue's CE atom to CE3 in the PDB file and the relevant RTP entries accordingly (see below). I also changed the hdb entry for the new CE3 atom (also below).<br>
<br>Relevant RTP lines:<br> CE3 opls_209 0.0 10<br> HE31 opls_140 0.0 11<br> HE32 opls_140 0.0 12<br> HE33 opls_140 0.0 13<br> CE1 opls_145 0.0 32<br> HE1 opls_146 0.0 33<br>
CE2 opls_145 0.0 34<br> HE2 opls_146 0.0 35<br> [bonds]<br> CE3 HE31<br> CE3 HE32<br> CE3 HE33<br> CE1 HE1<br> CE2 HE2<br><br>Relevant HDB lines:<br>3 4 HE3 CE3 SD CG1<br>
1 1 HE1 CE1 CD1 CZ<br>1 1 HE2 CE2 CD2 CZ<br><br>I thought this would cover everything, but I am receiving the following sort of error from pdb2gmx for each of the the three CE3 hydrogens(pdb2gmx -f 2H5Q.pdb -o 2H5Q_processed.gro -water tip3):<br>
<br>"WARNING: atom HE31 is missing in residue CH6 66 in the pdb file<br> You might need to add atom HE31 to the hydrogen database of building block CH6<br> in the file aminoacids.hdb (see the manual)"<br>
<br>I've looked at other examples in the aminoacids.hdb file and cannot figure out what I am missing here, it seems like my hdb rule should be adding 3 type 4 hydrogens named HE31, HE32, and HE33. I am assuming that the other hdb rules are OK, since they seemed to work fine before, as indicated by examining the gro file. I would sincerely appreciate any help you can offer. Thank you!<br>
<br>-Nathan<br><br clear="all"><br>-- <br>----------<br>J. Nathan Scott, Ph.D.<br>Postdoctoral Fellow<br>Department of Chemistry and Biochemistry<br>Montana State University<br>