Good morning,
I am encountering difficulties in using prepgen to build a modified
nucleic acid residue pair. the manifestation of the problem is that when
I attempt to use leap to build parameter files, and save a pdb to check
the structure, I have many atoms ontop of each other (especially
phosphates).
1. I have created parameter files and a prepgen file for the modified
nucleotide. Here is the .mc file associated with the prepgen file, which
is (I would guess) pretty much the same as any other .mc file for a
nucleic acid linkage inside a DNA helix:
HEAD_NAME P1
TAIL_NAME O2
MAIN_CHAIN O4
MAIN_CHAIN C10
MAIN_CHAIN C9
MAIN_CHAIN C8
OMIT_NAME H9
OMIT_NAME O7
OMIT_NAME H13
PRE_HEAD_TYPE O
POST_TAIL_TYPE P
CHARGE -1.0
That is, the head is a phosphate, the tail is an oxygen off a ribose, I
show the shortest-path linkage between the phosphate and the oxygen
ribose, omit the extra hydrogen from the ribose alcohol for the linkage
sake
I have pretty much the same file for the other modified residue.
2.) When attempting to construct the parameters in leap, I perform:
source leaprc.ff14SB
loadamberprep unit_1.prepin
loadamberparams unit_1.frcmod
loadamberprep unit_2.prepin
loadamberparams unit_2.frcmod
foo=loadpdb file_name.pdb
for unit_1 and 2 are the new nucleic acid residues, file_name.pdb is the
input geometry to which I would like to assign parameters. When I save a
pdb to look at it, the above description of overlapping atoms applies.
Moreover, in leap, when I load the pdb, there are many missing heavy
atoms in the leap record for each of the new units. Hence why I have
overlapping atoms.
3.) The mystery to me is the fact the PDB generated by prepgen shows the
correct structure (the default NEWPDB.PDB file that is generated) in all
regards. All the correct atoms are there. They are 1-1 with my generated
PDB structure.
4.) This would lead me to believe that I must have a mistake in my .mc
file listed above, that the connections are being made erroneously. I
assume to just post that, although I can imagine someone asking for any
of the other many commands involved in this complicated process (but for
the sake of brevity, I will leave it as this, since short emails=good).
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Received on Sun Oct 11 2015 - 09:00:03 PDT
