Dear user,
I have a problem with the CHCL3BOX
I want to use the chloroform as solvent so
I write this command
loadamberparams frcmod.chcl3
edit CHCL3BOX
and check CHCL3BOX
to control the molecules and it is all ok
then I save the pdb
savepdb CHCL3BOX box.pdb
It is possible to open this pdb with VMD, pymol, etc
but if I load with xleap
this file with
P=loadpdb box.pdb
I have these errors for all atoms
Created a new atom named: H1 within residue: .R<CL3 1>
Created a new atom named: C1 within residue: .R<CL3 1>
Created a new atom named: CL1 within residue: .R<CL3 1>
Created a new atom named: CL2 within residue: .R<CL3 1>
Created a new atom named: CL3 within residue: .R<CL3 1>
Added missing heavy atom: .R<CL3 1>.A<Cl 5>
Added missing heavy atom: .R<CL3 1>.A<C 2>
Added missing heavy atom: .R<CL3 1>.A<Cl 1>
Added missing heavy atom: .R<CL3 1>.A<Cl 4>
Created a new atom named: H1 within residue: .R<CL3 2>
Created a new atom named: C1 within residue: .R<CL3 2>
Created a new atom named: CL1 within residue: .R<CL3 2>
Created a new atom named: CL2 within residue: .R<CL3 2>
Created a new atom named: CL3 within residue: .R<CL3 2>
Added missing heavy atom: .R<CL3 2>.A<Cl 5>....
I want to use chloroform as solvent but before to start it is necessary
to solve this problem.
Then I try another way, I prepared a prep file for chloroform
loadamberprep chcl3.prep
edit CL3
no problem
check CL3 no problem
but after the solvatebox command with CHCL3BOX
and savepdb the new pdb gives the same problems.
There is someone that can help me with this problem?
silvia
--
Silvia Carlotto, Ph.D
Università degli Studi di Padova
Dipartimento di Scienze Chimiche
via Marzolo 1, 35131 Padova
Telefono: +390498275124
E-mail: silvia.carlotto.unipd.it
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Received on Fri Sep 18 2009 - 06:00:05 PDT
