AMBER Archive (2008)

Subject: Re: AMBER: connectivity problem

From: Junmei Wang (
Date: Wed Jan 09 2008 - 09:51:05 CST

Hi, Ram,
NEWPDB does not contain any connectivity information. If you want to know
the connectivity table, simply convert the prepi file to a mol2 file and
display the molecule with a graphic software. The command should be:
antechamber -fi prepi -fo mol2 -i input.prepi -o output.mol2 -at sybyl

If there is something wrong with the connectivity, manually revise the mol2
file (don't forget to change the number of bond on the line like " ???
??? 1 0 0"). Then take the modified mol2 file as input to
generate prepi file.

Good luck


On Jan 9, 2008 8:53 AM, rams rams <> wrote:

> Dear All,
> I have the following connectivity problem:
> I am using antechamber for generating .frcmod and .prep files for one of
> my inhibitor. If I compare the NEWPDB file of the inhibitor generated in
> antechamber and the original pdb file of the inhibitor which I extracted
> from the crystal structure reported (protein with inhibitor), the
> coordinates are exactly the same. But there is a connectivity lose between
> P(H2PO3) and C (CF2) in the NEWPDB. Despite of the lose of this
> connectivity, I continued doing LEaP and gas phase minimization, one of the
> P got attached to C (out of two) but the second one still remains as an
> isoloted species. Is there any way I can fix this problem I have the same
> connectivity problem between C and Br atoms in another inhibitor. Is this a
> common problem in using antechamber or any specific care has to be taken
> while doing antechamber.
> Thanks and Regards,
> Ram.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to