Dear Amber User,
Does anyone has cyclohexane solvent box available?
I try to build one, I have the final md.rst but I could not build the
periodic box by following David's advice, which shown below:
"Use ambpdb to convert the coordinates to pdb format, then read it back into
LEap and use the setBox command to make it periodic. Save it as on off file.
"
I output the .rst to pdb file, but the cyclohexane molecule is disperse. If
i read back into Leap, this is what happen. I have 117 residues. It
complaint the atoms are not in residue templates. And if I edit the
molecules, I only see boxes and it is without charges.
Creating new UNIT for residue: INT sequence: 117
Created a new atom named: C1 within residue: .R<INT 117>
Created a new atom named: H12 within residue: .R<INT 117>
Created a new atom named: H11 within residue: .R<INT 117>
Created a new atom named: C2 within residue: .R<INT 117>
Created a new atom named: H21 within residue: .R<INT 117>
Created a new atom named: H22 within residue: .R<INT 117>
Created a new atom named: C3 within residue: .R<INT 117>
Created a new atom named: H31 within residue: .R<INT 117>
Created a new atom named: H32 within residue: .R<INT 117>
Created a new atom named: C4 within residue: .R<INT 117>
Created a new atom named: H41 within residue: .R<INT 117>
Created a new atom named: H42 within residue: .R<INT 117>
Created a new atom named: C5 within residue: .R<INT 117>
Created a new atom named: H51 within residue: .R<INT 117>
Created a new atom named: H52 within residue: .R<INT 117>
Created a new atom named: C6 within residue: .R<INT 117>
Created a new atom named: H61 within residue: .R<INT 117>
Created a new atom named: H62 within residue: .R<INT 117>
total atoms in file: 2106
The file contained 2106 atoms not in residue templates
Any help is appreciated.
Andy
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Received on Mon Oct 17 2005 - 05:53:01 PDT
