I seem to be failing in putting a PDB file into leap; the manifestations
of this are having the wrong total charge and the wrong atom types.
1.) I have a PDB file that I input into leap, attached here as
start.pdb; the result is after.pdb
In leap, I enter
source leaprc.ff14SB
loadamberprep 1WA.prepin
loadamberparams 1WA.frcmod
loadamberprep 1W5.prepin
loadamberparams 1W5.frcmod
foo=loadpdb start.pdb
savepdb foo after.pdb
There are no error messages of any kind, at this point. The PDB
"after.pdb" looks fine; it represents my target structure, visually. I
do have a separate question, at this point in time; I assume that the
name "1W5" ahead of the .frcmod file indicates that a defined unit "1W5"
from the previous step gets those parameters? I have had some confusion
in looking at the manual/elementary tutorials in understanding what
binds a unit name to a particular parameter file (if one defines it and
not just uses the force field defaults, like ff14SB)
2.) When I attempt to bind parameters, I get (at least) two unusual
messages. The output after asking for saveamberparm foo prmtop inpcrd is:
Checking Unit.
WARNING: The unperturbed charge of the unit: -30.000006 is not zero.
-- ignoring the warning.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Could not find angle parameter: CT - OH - P
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
<1WA 24>: C5 C3 N4 C6
<1WA 24>: N4 N1 C3 N3
<1WA 24>: C1 C4 N1 C3
<1WA 24>: N1 N2 C1 O1
<1WA 24>: N5 N2 C2 N3
<1WA 24>: C2 H3 N5 H4
<1WA 24>: C5 H1 C4 N1
<1WA 24>: C4 H2 C5 N4
<1W5 25>: C5 C3 C4 C6
<1W5 25>: C4 C2 C3 H1
<1W5 25>: C3 C1 C2 N3
<1W5 25>: C2 N2 C1 N1
<1W5 25>: C5 C1 N1 H2
<1W5 25>: C4 N1 C5 O1
<1W5 25>: C1 H3 N2 H4
<1W5 25>: C2 O2 N3 O3
total 202 improper torsions applied
96 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Parameter file was not saved.
I have slightly modified this; the error output for the dihedrals (1W5
and 1WA) actually repeated many, many times, but I just left one example
to keep this email short.
There are two oddities I noticed. For one, the charge is -30. Given that
there are 16 nucleotide base pairs, I would say that the total charge is
-32. I believe that there are 2 more negative charges at the 5' ends,
which should give a total of -34. I am thus doing something wrong on
this basis.
Furthermore, the error message says I lack CT-OH-P bond parameters.
Indeed I do lack them; what I do not understand is why I need them. This
would imply I have an alcoholic oxygen next to a phosphate; I do not. On
looking at the after.pdb file, I see no such alcohols next to phosphorus
atoms.
3.) My guess is that I have somehow messed up my .prepin file. It seems
like the hydrogen which gets omitted in my .mc file causes the oxygen to
which it was attached to be an OH type instead of a OS type:
0 0 2
This is a remark line
molecule.res
1WA INT 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.523 111.21 .0 .00000
4 P1 P M 3 2 1 1.540 111.208 -180.000 1.455874
5 O5 O2 E 4 3 2 1.504 3.424 161.162 -0.829325
6 O6 O2 E 4 3 2 1.522 122.567 34.322 -0.829325
7 O4 OS M 4 3 2 1.681 109.856 162.745 -0.571566
8 C10 CT M 7 4 3 1.402 121.367 158.424 0.206395
9 H11 H1 E 8 7 4 1.104 111.381 -69.133 0.037563
10 H12 H1 E 8 7 4 1.105 106.692 173.481 0.037563
11 C9 CT M 8 7 4 1.520 114.452 54.854 0.062706
12 O3 OS S 11 8 7 1.445 106.403 171.959 -0.414514
13 C6 CT 3 12 11 8 1.393 110.260 -138.373 0.255268
14 N4 N* S 13 12 11 1.471 111.710 -95.506 -0.114967
15 C3 CB S 14 13 12 1.355 123.529 -99.067 0.163985
16 N1 N* B 15 14 13 1.358 107.343 176.179 -0.147744
17 C1 C B 16 15 14 1.436 120.928 179.299 0.756008
18 O1 O E 17 16 15 1.216 118.333 -179.711 -0.617414
19 N2 NC S 17 16 15 1.353 114.056 0.444 -0.767534
20 C2 CQ B 19 17 16 1.332 119.503 -0.582 0.891821
21 N3 NC E 20 19 17 1.350 129.053 0.451 -0.532055
22 N5 N2 B 20 19 17 1.367 116.006 -178.214 -0.881115
23 H3 H E 22 20 19 1.009 116.357 -14.982 0.429451
24 H4 H E 22 20 19 1.009 116.937 -164.589 0.429451
25 C4 CA B 16 15 14 1.392 109.300 -0.614 -0.131009
26 H1 H4 E 25 16 15 1.082 120.849 -179.762 0.203972
27 C5 CA S 25 16 15 1.352 106.903 0.202 -0.122096
28 H2 H4 E 27 25 16 1.090 132.119 179.699 0.234265
29 H5 H2 E 13 12 11 1.097 108.080 150.550 0.109761
30 C7 CT B 13 12 11 1.523 105.894 27.744 -0.117244
31 H6 HC E 30 13 12 1.098 107.895 89.265 0.072905
32 H7 HC E 30 13 12 1.097 113.685 -150.380 0.072905
33 H10 H1 E 11 8 7 1.101 110.843 -69.654 0.076439
34 C8 CT M 11 8 7 1.538 114.072 53.963 0.140458
35 H8 H1 E 34 11 8 1.103 109.349 -3.085 0.086537
36 O2 OH M 34 11 8 1.405 112.678 -125.492 -0.647418
LOOP
C5 N4
N3 C3
C8 C7
IMPROPER
C5 C3 N4 C6
N4 N1 C3 N3
C1 C4 N1 C3
N1 N2 C1 O1
N5 N2 C2 N3
C2 H3 N5 H4
C5 H1 C4 N1
C4 H2 C5 N4
DONE
STOP
My prepin file labels atom 36 as an OH type. This atom is part of the
DNA polymerization; its original hydrogen gets an OMIT NAME in my .mc
file. In my .ac file, naturally, I have atom 35 (the oxygen before the
hydrogen) as an OH type:
CHARGE -1.00 ( -1 )
Formula: H13 C10 N5 O7 P1
ATOM 1 C1 MOL 1 4.595 -1.242 0.530 0.748700 C
ATOM 2 C2 MOL 1 4.638 1.076 0.483 0.883200 CQ
ATOM 3 C3 MOL 1 2.725 0.159 -0.143 0.162400 CB
ATOM 4 O1 MOL 1 5.014 -2.371 0.699 -0.623500 O
ATOM 5 N1 MOL 1 3.245 -1.078 0.069 -0.149200 N*
ATOM 6 N2 MOL 1 5.255 -0.078 0.729 -0.775100 NC
ATOM 7 N3 MOL 1 3.379 1.291 0.047 -0.537300 NC
ATOM 8 C4 MOL 1 2.283 -2.039 -0.230 -0.132300 CA
ATOM 9 H1 MOL 1 2.500 -3.094 -0.122 0.202000 H4
ATOM 10 C5 MOL 1 1.175 -1.375 -0.630 -0.123300 CA
ATOM 11 H2 MOL 1 0.195 -1.720 -0.959 0.232000 H4
ATOM 12 N4 MOL 1 1.455 -0.007 -0.584 -0.116100 N*
ATOM 13 N5 MOL 1 5.383 2.206 0.672 -0.889800 N2
ATOM 14 H3 MOL 1 6.239 2.096 1.195 0.425300 H
ATOM 15 H4 MOL 1 4.882 3.080 0.726 0.425300 H
ATOM 16 C6 MOL 1 0.534 1.109 -0.847 0.252800 CT
ATOM 17 H5 MOL 1 1.190 1.986 -0.918 0.108700 H2
ATOM 18 C7 MOL 1 -0.338 0.880 -2.074 -0.118400 CT
ATOM 19 H6 MOL 1 -0.539 1.857 -2.532 0.072200 HC
ATOM 20 H7 MOL 1 0.124 0.231 -2.828 0.072200 HC
ATOM 21 C8 MOL 1 -1.631 0.274 -1.529 0.139100 CT
ATOM 22 H8 MOL 1 -2.511 0.749 -1.995 0.085700 H1
ATOM 23 O2 MOL 1 -1.661 -1.112 -1.758 -0.653800 OH
ATOM 24 H9 MOL 1 -2.468 -1.422 -1.269 0.479000 HO
ATOM 25 O3 MOL 1 -0.346 1.312 0.214 -0.418600 OS
ATOM 26 C9 MOL 1 -1.594 0.627 -0.033 0.062100 CT
ATOM 27 H10 MOL 1 -1.616 -0.302 0.557 0.075700 H1
ATOM 28 C10 MOL 1 -2.698 1.574 0.408 0.204400 CT
ATOM 29 H11 MOL 1 -2.598 1.758 1.492 0.037200 H1
ATOM 30 H12 MOL 1 -2.537 2.535 -0.114 0.037200 H1
ATOM 31 O4 MOL 1 -3.993 1.149 0.079 -0.577200 OS
ATOM 32 P1 MOL 1 -4.564 -0.361 0.548 1.441800 P
ATOM 33 O5 MOL 1 -6.065 -0.276 0.519 -0.837500 O2
ATOM 34 O6 MOL 1 -3.745 -1.420 -0.175 -0.837500 O2
ATOM 35 O7 MOL 1 -4.048 -0.386 2.137 -0.789400 OH
ATOM 36 H13 MOL 1 -4.803 -0.105 2.665 0.435000 HO
If this is the nature of the problem, the solution is clear (I change
the OH in my .ac file to a OS). This is fine, but I want to clarify that
this is the case (this is a seeming missing step in the prepgen
tutorial, to my very naive mind?).
If this is true, a corollary is that I have to change all the parameters
of the OH, manually, to be what they are for an OS? As well as do a
charge-fitting with a constraint to have no charge assigned to the
hydrogen atom?
--
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Visiting Associate Professor of Chemistry
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Fri Oct 16 2015 - 16:30:03 PDT
