AMBER Archive (2008)

Subject: Re: AMBER: connectivity problem

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jan 10 2008 - 09:27:07 CST

Hi Ram,
NEWPDB.PDB dose not have any connectivity information. Antechamber writes
out this file as a memo of how atomic sequence being changed to generate the
prepin file. The input connectivity information (from an ac or mol2 file) is
100% incorporated into the prepin file. In another word, your prepin file
should be good if the input connectivity is good.

If there is no connectivity information in a pdb file, programs including
antechamber and vmd use their own ways to judge the connectivity mainly
based on the distances. If the input geometry is not good enough, mistakes
may be happen. This is the reason we suggest to use mol2 or ac as input in
antechamber. If one use pdb without connectivity, he or she should be very
careful and manually revise the connectivity table if error occurs.

Best

Junmei

On Jan 9, 2008 11:04 PM, rams rams <rams.crux_at_gmail.com> wrote:

> 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,
> Ram.
>
>
> On Jan 9, 2008 9:21 PM, Junmei Wang <junmwang_at_gmail.com> 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 < rams.crux_at_gmail.com> 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.
> > >
> >
> >
>

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