What if you don't loadpdb, just save the model as pdb? Then compare that
pdb to yours to learn what leap thinks.
Bill
On 11/10/17 9:18 PM, Saikat Pal wrote:
> Dear Sir,Thank you , for your kind response.I got the pdb of urea.But when I load the pdb file this error has been shown:
> > loadamberparams frcmod.urea
> Loading parameters: /home/saikat/AMBER/amber14//dat/leap/parm/frcmod.urea
> Reading force field modification type file (frcmod)
> Reading title:
> Parameters of N - C - N angle and corresponding force const.
>> loadoff 8Mureabox.off
> Loading library: /home/saikat/AMBER/amber14//dat/leap/lib/8Mureabox.off
> Loading: UREABOX
>> m=loadpdb urea-gaff.pdb
> Loading PDB file: ./urea-gaff.pdb
> Enter zPdbReadScan from call depth 0.
> Exit zPdbReadScan from call depth 0.
> Matching PDB residue names to LEaP variables.
> (Residue 0: URE, Terminal/last, was not found in name map.)
> Unknown residue: URE number: 0 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: URE sequence: 1
> Created a new atom named: C within residue: .R<URE 1>
> Created a new atom named: N1 within residue: .R<URE 1>
> Created a new atom named: N2 within residue: .R<URE 1>
> Created a new atom named: O within residue: .R<URE 1>
> Created a new atom named: H1 within residue: .R<URE 1>
> Created a new atom named: H2 within residue: .R<URE 1>
> Created a new atom named: H3 within residue: .R<URE 1>
> Created a new atom named: H4 within residue: .R<URE 1>
> total atoms in file: 8
> The file contained 8 atoms not in residue templates
>
> Thanks And Regards,
> Saikat
>
> On Friday 10 November 2017, 6:49:01 PM IST, David A Case <david.case.rutgers.edu> wrote:
>
> On Fri, Nov 10, 2017, Saikat Pal wrote:
>
>> I want to save UREA PDB file from xleap. Is it
>> possible ?? what is the command for ureabox(8M).
> Should be just "savePdb UREABOX ureabox.pdb" Does that not work?
>
> ....dac
>
>
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Received on Sat Nov 11 2017 - 00:00:03 PST
