I apologize. In my efforts to not deluge you with details and conserve
time, I have made things worse.
I have a pdb file from a crystal structure of a DNA helix (of sorts); I
would be happy to attach it in a private email. I have taken the
following steps:
0.) Pursuant to the manual's advice on PDB prepation, I used the --dry
command to get rid of the unnecessary waters, deleted the hydrogens.
1.) The original crystal structure used bromouracil for the sake of
analysis/crystallization; my intended target is not going to have it. I
thus edited the bromouracil tags to be a thymine tag. The original pdb
text was:
HETATM 37 N1 BRU A 3 32.558 22.286 -1.781 1.00
22.63 N
HETATM 38 C2 BRU A 3 32.124 23.223 -0.851 1.00
20.27 C
HETATM 39 N3 BRU A 3 32.955 24.056 -0.249 1.00
19.85 N
HETATM 40 C4 BRU A 3 34.250 24.037 -0.508 1.00
21.50 C
HETATM 41 C5 BRU A 3 34.780 23.081 -1.478 1.00
21.92 C
HETATM 42 C6 BRU A 3 33.870 22.243 -2.071 1.00
22.63 C
HETATM 43 O2 BRU A 3 30.938 23.271 -0.599 1.00
20.66 O
HETATM 44 O4 BRU A 3 35.008 24.808 0.072 1.00
22.08 O
HETATM 45 BR BRU A 3 36.615 23.009 -1.896 0.31
23.08 BR
HETATM 46 C1' BRU A 3 31.586 21.365 -2.421 1.00
22.06 C
HETATM 47 C2' BRU A 3 30.813 21.982 -3.566 1.00
22.93 C
HETATM 48 C3' BRU A 3 31.554 21.535 -4.800 1.00
25.02 C
HETATM 49 C4' BRU A 3 32.157 20.218 -4.391 1.00
23.77 C
HETATM 50 O3' BRU A 3 30.741 21.545 -5.964 1.00
29.59 O
HETATM 51 O4' BRU A 3 32.284 20.280 -2.981 1.00
21.98 O
HETATM 52 C5' BRU A 3 33.541 19.974 -4.929 1.00
27.91 C
HETATM 53 O5' BRU A 3 33.874 18.603 -4.953 1.00
24.68 O
HETATM 54 P BRU A 3 35.234 18.123 -4.313 1.00
29.91 P
HETATM 55 OP1 BRU A 3 35.562 16.726 -4.619 1.00
29.07 O
HETATM 56 OP2 BRU A 3 36.305 19.061 -4.598 1.00
30.08 O
and I modified it to
HETATM 61 N1 DT A 3 32.558 22.286 -1.781 1.00
22.63 N
HETATM 62 C2 DT A 3 32.124 23.223 -0.851 1.00
20.27 C
HETATM 63 N3 DT A 3 32.955 24.056 -0.249 1.00
19.85 N
HETATM 64 C4 DT A 3 34.250 24.037 -0.508 1.00
21.50 C
HETATM 65 C5 DT A 3 34.780 23.081 -1.478 1.00
21.92 C
HETATM 66 C6 DT A 3 33.870 22.243 -2.071 1.00
22.63 C
HETATM 67 O2 DT A 3 30.938 23.271 -0.599 1.00
20.66 O
HETATM 68 O4 DT A 3 35.008 24.808 0.072 1.00
22.08 O
HETATM 69 C7 DT A 3 36.615 23.009 -1.896 0.31
23.08 C
HETATM 70 C1' DT A 3 31.586 21.365 -2.421 1.00
22.06 C
HETATM 71 C2' DT A 3 30.813 21.982 -3.566 1.00
22.93 C
HETATM 72 C3' DT A 3 31.554 21.535 -4.800 1.00
25.02 C
HETATM 73 C4' DT A 3 32.157 20.218 -4.391 1.00
23.77 C
HETATM 74 O3' DT A 3 30.741 21.545 -5.964 1.00
29.59 O
HETATM 75 O4' DT A 3 32.284 20.280 -2.981 1.00
21.98 O
HETATM 76 C5' DT A 3 33.541 19.974 -4.929 1.00
27.91 C
HETATM 77 O5' DT A 3 33.874 18.603 -4.953 1.00
24.68 O
HETATM 78 P DT A 3 35.234 18.123 -4.313 1.00
29.91 P
HETATM 79 OP1 DT A 3 35.562 16.726 -4.619 1.00
29.07 O
HETATM 80 OP2 DT A 3 36.305 19.061 -4.598 1.00
30.08 O
That is to say, I modified the Br atom to be a carbon atom to go from a
bromouracil to a methyl (relying on leap to fill out the necessary
hydrogens later). I also changed the label from BRU to DT. I did not
change HETATM, but my understanding is that this does not matter (nor
did it seem to when I tested it, but the ultimate problem may contradict
this). There were two bromouracils, as residues 3 and 19.
2.) There were some covalently bound "ligands" in my crystal structure;
they are holding the location of where normal nucleotides would be in
every way (connection with the helix, sandwiched in-between aromatic
discs of DNA). They are called, in the PDB, 1W5 and 1WA. I thus created
parameter files for them. I am not at the point that I am *applying* the
parameters, so I assume this information is extraneous. However, I did
make sure to note the atom types in my parameter files, made sure to
match them to a drawing of the molecule.
3.) I created a prepgen input. Given that the connections in this DNA
are identical to that of standard DNA, I created a prepin file based on
the following MC file:
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
the prepin file seems to have been made correctly. I am happy to post
this as well, just trying not to deluge with information which I *think*
is irrelevant.
4.) With the information of the atom types in my parameters/prepgen, I
edited the PDB file to have the atom types of 1WA and 1W5 be the same
labels as what they are in my parameter/prepgen files. There seems to be
no problem with this. I don't think 1W5 or 1WA have anything to do
5.) This is where the fun starts. In leap, I enter the following
commands without any issues:
source leaprc.ff14SB
loadamberprep 1WA.prepin
loadamberparams 1WA.frcmod
loadamberprep 1W5.prepin
loadamberparams 1W5.frcmod
At this point, I load the pdb via
foo=loadpdb foo.pdb
and I receive the following warning messages:
Loading PDB file: ./3.pdb
(starting new molecule for chain )
(starting new molecule for chain A)
(starting new molecule for chain )
(starting new molecule for chain B)
Created a new atom named: P within residue: .R<DA5 4>
Created a new atom named: OP1 within residue: .R<DA5 4>
Created a new atom named: OP2 within residue: .R<DA5 4>
Created a new atom named: P within residue: .R<DA5 20>
Created a new atom named: OP1 within residue: .R<DA5 20>
Created a new atom named: OP2 within residue: .R<DA5 20>
total atoms in file: 876
Leap added 162 missing atoms according to residue templates:
150 H / lone pairs
12 unknown element
The file contained 6 atoms not in residue templates
6.) I was perplexed why there was any need to add in new atoms in one
residue. I am unsure what the DA*5* means (well, the 5 in particular).
There should not be a need to, if it was true that I understood what's
going on. Residues 4 and 20 both follow the former bromouracils, which I
view as conspicuous. This implies I have done something inadequate
regarding the bromouracils to thymine transformation?
7.) If one views the file created after leap adds these atoms (by saving
the pdb from leap after the last commands entered), there are 6 Ho atoms
added to the system. Two are placed at terminal ribose alcohols, four
are around phosphates.
On 10/14/15 4:26 PM, David A Case wrote:
> On Wed, Oct 14, 2015, Robert Molt wrote:
>> I was hoping to please be advised where in the documentation it
>> clarifies when leap chooses to add an Ho atom.
>> In my particular case, I see Ho atoms added to non-terminal phosphates
>> as well as to alcohol groups coming off of terminal ribose units. I am
>> unsure what causes leap to add these to my PDB (it leaves other
>> phosphates in the DNA backbone alone, just some get a Ho).
>>
>> These are the mysterious atoms that entered my produced PDB file that I
>> formerly thought were resultant from a prepgen error.
> As you know, we have serious communication problems here. Can you provide a
> concrete (simple) example: give *all* the files and the *exact commands* you
> are using, so that we can try to reproduce the behavior. In particular, I
> don't really understand how you are creating the PDB file that has
> the extra atoms.
>
> As I have said before, LEaP is just a bookkeeping program at heart. My best
> guess is that there is an atom in the library you are loading that is *not*
> in the PDB file you are loading. This is the only scenario I can readily
> think of where there would be atoms in an (output) PDB file that were not
> present in the input PDB file. But since I don't know what libraries you are
> loading, nor what PDB file you are loading, nor what commands you are giving
> to LEaP, it's just really hard to give good advice.
>
> ...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
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 Wed Oct 14 2015 - 15:30:03 PDT
