Hey Gromacs Users,<br> I am trying to convert the zwitterionic form of glycine into a top and gro file from the pdb, while I appear to be able to do this with some efficiency by PRODRG is there a way to do this that keeps all my hydrogens in the same locations? This gets more complicated when I try and perform a similar thing on the anion, as I can generate the # of hydrogens etc. but I can't get it to freeze the hydrogen locations. Is there a way to generate the .gro and .top files directly from a PDB?
<br>Best,<br>Craig<br><br>Anionic Glycine PDB<br>REMARK 888<br>REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)<br>TITLE /glab/d1/craig/.schrodinger/tmp/12031/_mmoddat2<br>MODEL 1<br>HETATM 1 C1 UNK 900
0.315 -1.043 0.000 1.00 0.00 C<br>HETATM 2 C2 UNK 900 0.304 0.522 0.000 1.00 0.00 C<br>HETATM 3 N1 UNK 900 -1.016 -1.711 0.000 1.00 0.00 N<br>HETATM 4 O1 UNK 900
1.456 1.075 0.000 1.00 0.00 O1-<br>HETATM 5 O2 UNK 900 -0.850 1.079 0.000 1.00 0.00 O<br>HETATM 6 H1 UNK 900 0.885 -1.385 0.880 1.00 0.00 H<br>HETATM 7 H2 UNK 900
0.885 -1.385 -0.880 1.00 0.00 H<br>HETATM 8 H3 UNK 900 -1.520 -1.279 0.789 1.00 0.00 H<br>HETATM 9 H4 UNK 900 -1.520 -1.279 -0.789 1.00 0.00 H<br>CONECT 1 2 3 6 7
<br>CONECT 2 1 4 5<br>CONECT 2 5<br>CONECT 3 1 8 9<br>CONECT 4 2<br>CONECT 5 2<br>CONECT 5 2<br>CONECT 6 1<br>CONECT 7 1<br>CONECT 8 3<br>CONECT 9 3<br>
ENDMDL<br>END <br><br>