AMBER Archive (2006)

Subject: Re: AMBER: What's going wrong when I use antechamber dealing with lipid molecular?

From: Fenghui Fan (fenghui_fan_at_yahoo.com)
Date: Wed Dec 06 2006 - 20:51:41 CST

In the command, try add -j 0 and it should works.

In addition, what is your POPG molecule?

Best regards.

Fenghui Fan

--- ²άΘ½ <tomcao_at_mail.bnu.edu.cn> wrote:

> Hi all
>
> I'm using AMBER9.0 to simulate a protein-membrane
> system.Because I've no idea
> about how to set OPLS simulation parameters for
> lipid bilayer(which question I've
> already raised before this), I'm planning to use
> antechamber dealing with lipid
> such as one POPG molecular to obtain necessary
> parameters for further simulation
> with sander. But when I use antechamber to deal with
> one POPG molecular(without
> H)"antechamber -i popg.pdb -fi pdb -o popg.prepin
> -fo prepi -c bcc", program goes
> wrong giving message like this:
>
> Warning:the assigned bond types may be wrong,please:
> 1 double check the structure(the connectivity)
> and/or
> 2 adjust atom valence penalty parameters in APS.DAT,
> and/or
> 3 increase MAXVASTATE in define.h and recompile
> bondtype.C
> 4 increase PSCUTOFF in define.h and recompile
> bondtype.C
> Error:cannot run "/home/amber/exe/bondtype -i
> ANTECHAMBER_BOND_TYPE.ACO -o
> ANTECHAMBER_BOND_TYPE.AC -f ac -j full" in
> judgebondtype( ) of antechamber.c
> properly, exit
>
> I'm a new for amber and I'm so confused. Could you
> tell me what's going wrong and
> how to deal with this problem?
> Thanks a lot!
> Ran Cao
>
>
>
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