AMBER Archive (2009)

Subject: [AMBER] PROBLEM WITH CHCL3BOX pdb

From: Silvia Carlotto (silvia.carlotto_at_unipd.it)
Date: Fri Sep 18 2009 - 07:49:12 CDT

 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_at_unipd.it
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