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 Fri Nov 10 2017 - 21:30:02 PST
