Hey Gromacs Users,
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?
Best,
Craig
Anionic Glycine PDB
REMARK 888
REMARK 888 WRITTEN BY MAESTRO (A PRODUCT OF SCHRODINGER, LLC)
TITLE /glab/d1/craig/.schrodinger/tmp/12031/_mmoddat2
MODEL 1
HETATM 1 C1 UNK 900 0.315 -1.043 0.000 1.00 0.00
C
HETATM 2 C2 UNK 900 0.304 0.522 0.000 1.00 0.00
C
HETATM 3 N1 UNK 900 -1.016 -1.711 0.000 1.00 0.00
N
HETATM 4 O1 UNK 900 1.456 1.075 0.000 1.00 0.00
O1-
HETATM 5 O2 UNK 900 -0.850 1.079 0.000 1.00 0.00
O
HETATM 6 H1 UNK 900 0.885 -1.385 0.880 1.00 0.00
H
HETATM 7 H2 UNK 900 0.885 -1.385 -0.880 1.00 0.00
H
HETATM 8 H3 UNK 900 -1.520 -1.279 0.789 1.00 0.00
H
HETATM 9 H4 UNK 900 -1.520 -1.279 -0.789 1.00 0.00
H
CONECT 1 2 3 6 7
CONECT 2 1 4 5
CONECT 2 5
CONECT 3 1 8 9
CONECT 4 2
CONECT 5 2
CONECT 5 2
CONECT 6 1
CONECT 7 1
CONECT 8 3
CONECT 9 3
ENDMDL
END
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
