Re: AMBER: connectivity problem

From: rams rams <>
Date: Thu, 10 Jan 2008 10:34:41 +0530

Hi Junmei Wang,

Thanks for your suggestion. I did modified the mol2 file as you suggested
and then used the modified mol2 file as an input file to generate the prep
file but still the problem remained the same though the modified mol2 file
did showed the connectivity, the newpdb created by antechamber is not
showing any connectivity. It is not just the visualization program (VMD)
problem I guess because, in one case it is showing the connectivity and in
the other case it doesn't (though the coordintes are exactly the same in
both the cases).

Thanks and regards,

On Jan 9, 2008 9:21 PM, Junmei Wang <> wrote:

> 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
> Junmei
> 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
Received on Sun Jan 13 2008 - 06:07:10 PST
Custom Search