General problem: leap “incorrectly” reads in my PDB file. I say “incorrectly” because I am sure the fault is actually mine.
System under consideration: I have a system with both a protein and a DNA helix. I have amino acids numbered 43-318; I then have nucleic acids numbered 1-21, twice (once for each strand). I have attached the relevant PDB file in this email. In particular, the amino acids are numbered 43-318 in the file, and then the nucleic acids are numbered 1-21 for the first strand, then 1-21 again for the second strand.
Commands issued:
xleap
source leaprc.ff14SB
piggy=loadpdb 2.pdb
Symptoms of the problem:
leap responded with
> piggy=loadpdb 2.pdb
Loading PDB file: ./2.pdb
Enter zPdbReadScan from call depth 0.
-- residue 328: duplicate [ C1'] atoms (total 2)
-- residue 328: duplicate [ C2] atoms (total 2)
-- residue 328: duplicate [ C2'] atoms (total 2)
-- residue 328: duplicate [ C3'] atoms (total 2)
-- residue 328: duplicate [ C4] atoms (total 2)
-- residue 328: duplicate [ C4'] atoms (total 2)
-- residue 328: duplicate [ C5] atoms (total 2)
-- residue 328: duplicate [ C5'] atoms (total 2)
-- residue 328: duplicate [ C6] atoms (total 2)
-- residue 328: duplicate [ CM2] atoms (total 2)
-- residue 328: duplicate [ N1] atoms (total 2)
-- residue 328: duplicate [ N3] atoms (total 2)
-- residue 328: duplicate [ N4] atoms (total 2)
-- residue 328: duplicate [ O2] atoms (total 2)
-- residue 328: duplicate [ O2'] atoms (total 2)
-- residue 328: duplicate [ O3'] atoms (total 2)
-- residue 328: duplicate [ O4'] atoms (total 2)
-- residue 328: duplicate [ O5'] atoms (total 2)
-- residue 328: duplicate [ OP1] atoms (total 2)
-- residue 328: duplicate [ OP2] atoms (total 2)
-- residue 328: duplicate [ P] atoms (total 2)
-- residue 329: duplicate [ C1] atoms (total 2)
-- residue 329: duplicate [ C2] atoms (total 2)
-- residue 329: duplicate [ C3] atoms (total 2)
-- residue 329: duplicate [ C4] atoms (total 2)
-- residue 329: duplicate [ C5] atoms (total 2)
-- residue 329: duplicate [ O3] atoms (total 2)
-- residue 329: duplicate [ O4] atoms (total 2)
-- residue 329: duplicate [ O5] atoms (total 2)
-- residue 329: duplicate [ OP2] atoms (total 2)
…etc., until,
-- residue 156: duplicate [ NH1] atoms (total 2)
-- residue 156: duplicate [ NH2] atoms (total 2)
Warning: Atom names in each residue should be unique.
(Same-name atoms are handled by using the first
occurrence and by ignoring the rest.
Frequently duplicate atom names stem from alternate
conformations in the PDB file.)
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/beginning, seq. number: 0 to: NALA.
(Residue 1: LEU, Nonterminal, was not found in name map.)
(Residue 2: TYR, Nonterminal, was not found in name map.)
(Residue 3: GLU, Nonterminal, was not found in name map.)
As far as I can tell, I do not have duplicate atoms. Suffice it to say that it is all downhill from here on out in loading the file.
Specific questions:
1.) Should numbering in a pdb file for leap be consecutive? i.e., 43-360, in my case?
2.) I assume to ignore the “was not found in name map,” based on other Amberposts which recount this as a “trivial” error that is inconsequential
3.) Eventually, I get a leap dialogue of
Joining DG - DC
Joining DC - DG
Creating new UNIT for residue: OMC sequence: 328
One sided connection. Residue: missing connect0 atom.
Created a new atom named: N1 within residue: .R<OMC 328>
Created a new atom named: C2 within residue: .R<OMC 328>
Created a new atom named: N3 within residue: .R<OMC 328>
The first two lines show it is joining various DNA nucleic acids as “connected.” The next few lines alarm me: this should be the end of making connections? I gather my PDB is missing a TER flag?
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Received on Wed Oct 23 2019 - 19:30:02 PDT
