Hello,
Thank you Dr.Case, the water issue has been resolved, but now there is a
problem reading ethanol. what I have done:
1) I defined one ethanol in the pdb file, loading the mol2 and frcmod in
tleap and sourcing leaprc.gaff >> successful
2) then defined another ethanol in the pdb (all coordination taking from
packmol box), loading the same files in 1 the error is
>>-- residue 1: duplicate [ L] atoms (total 9)
-- residue 2: duplicate [ L] atoms (total 9)
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.
(Residue 0: G B, Terminal/last, was not found in name map.)
Unknown residue: G B number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
(Residue 1: G B, Terminal/last, was not found in name map.)
Unknown residue: G B number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: G B sequence: 1
Created a new atom named: L within residue: .R<G B 1>
Creating new UNIT for residue: G B sequence: 2
Created a new atom named: L within residue: .R<G B 2>
total atoms in file: 18
The file contained 2 atoms not in residue templates
3) I created two separate mol2 files for each ethanol coordination, loaded
them and then combined them, and change the pdb to be readable by tleap >>
worked fine and generated *3.pdb*, 3.prmtop, and 3.inpcrd for both.
4) I have *two* questions:
- when I loaded *3.pdb* again in tleap, it was not readable!!
although I did source leaprc.gaff, *Why is that?*
>>Unknown residue: MOL number: 0 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: MOL number: 1 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: MOL sequence: 1
Created a new atom named: C1 within residue: .R<MOL 1>
Created a new atom named: C2 within residue: .R<MOL 1>
Created a new atom named: H1 within residue: .R<MOL 1>
Created a new atom named: H2 within residue: .R<MOL 1>
Created a new atom named: H3 within residue: .R<MOL 1>
Created a new atom named: H4 within residue: .R<MOL 1>
Created a new atom named: H5 within residue: .R<MOL 1>
Created a new atom named: H6 within residue: .R<MOL 1>
Created a new atom named: O1 within residue: .R<MOL 1>
Creating new UNIT for residue: MOL sequence: 2
Created a new atom named: C1 within residue: .R<MOL 2>
Created a new atom named: C2 within residue: .R<MOL 2>
Created a new atom named: H1 within residue: .R<MOL 2>
Created a new atom named: H2 within residue: .R<MOL 2>
Created a new atom named: H3 within residue: .R<MOL 2>
Created a new atom named: H4 within residue: .R<MOL 2>
Created a new atom named: H5 within residue: .R<MOL 2>
Created a new atom named: H6 within residue: .R<MOL 2>
Created a new atom named: O1 within residue: .R<MOL 2>
total atoms in file: 18
The file contained 18 atoms not in residue templates
5) I want to include ~2800 ethanol molecules, *How can** tleap read the pdb
for all ethanol molecules?*
Thank you,
Sanaa
On Tue, Sep 19, 2017 at 3:39 AM, David A Case <david.case.rutgers.edu>
wrote:
> On Mon, Sep 18, 2017, Sanaa ALAbbad wrote:
>
> > 2) changing the water residue name from HOH to WAT, HETATOM to ATOM, TER
> > each molecule (this will require a lot of work)
>
> You should not need to do any of the above steps: tleap should be just fine
> with the original file: it knows that HOH and WAT are the same, doesn't
> care
> about HETATM vs ATOM, and does not require TER cards between waters.
>
> ....dac
>
>
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Received on Tue Sep 19 2017 - 16:00:01 PDT
