AMBER Archive (2008)

Subject: Re: AMBER: A problem about antechamber

From: Junmei Wang (
Date: Tue Jan 08 2008 - 16:19:15 CST

Your molecule still has open valences. Are you sure the amide nitrogen does
not have any hydrogen atom? In another word, they are negative charged?


On Jan 8, 2008 10:03 AM, ë <> wrote:

> Dear someone who may concern this letter,
> I have used the antechamber to deal with a carbohydrate. But there are
> still some problems. So I deleted the residue one by one to find which bond
> result this problem. And found some bonds with unappropriate bond type.
> I think this problem is really hard. I have added H and checked the
> conectivity of the molecular for several times. But I can not solve this
> problems.
> Would you like to help me to solve this problem?
> I have attached the pdb file to this mail.
> ------------------------------
> Ż䴫ףԺؿ<>
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