AMBER Archive (2008)

Subject: AMBER: Re: AMBER: Re: Re: AMBER: problems form the pdb to the mol2

From: Junmei Wang (junmwang_at_gmail.com)
Date: Wed Jun 25 2008 - 11:29:44 CDT


The key of using antechamber properly is to prepare a good input molecule
(no open valence, reasonable geometry if no connectivity table provided
...). If some atoms are missing, antechamber may not assign atom
types/bond types correctly, no matter the input is mol2 or pdb or other
format. As a matter of fact, if the input molecule is good, mol2 and prepi
all work fine.

Best

Junmei

2008/6/25 Cyril Bauvais <bauvais_at_itodys.jussieu.fr>:

> what about this following protocol ?
>
> don't use prepi but top and crd files.
> Try this :
>
> - use parmchk to create frcmod for your ligand (mol2) file
> and in xleap :
> - LIG = loadmol2 ligand.mol2 (and load frcmod)
> - REC = loadpdb rec.pdb
> - CPX = combine {REC LIG}
> (check REC and edit REC to check if everything seems ok)
> - saveamberparm CPX cpx.top cpx.crd
>
>
>
> Rilei Yu a crit :
> > Thanks for your reply!
> > When I plan to run MD on the whole system of the
> > receptor-ligand,usually, firstly I want to use antechamber to obtain
> > the ligand.prepin file and ligand.frcmod file. Then I can obtain the
> > .prmtop and .inpcrd file of the whole complex in Xleap/tleap.
> > Now, if I save the ligand using mol2 format and save the receptor
> > using the pdb format, how can I save the receptor -ligand in a file
> > and run the MD on the whole complex? Maybe I misunderstand your
> > suggestions. Can you more explicitly elaborate your advices or methods
> > please? I am really interested in your suggestions!
> > Thanks for your suggestion again!
> >
> >
> > */Cyril Bauvais <bauvais_at_itodys.jussieu.fr>/* д
> >
> > Also, if you have Sybyl software and use it to prepare files for
> Amber
> > calculation, it can be easier to keep mol2 files for ligand and pdb
> > format for receptor (if it is a problem receptor - ligand)...
> >
> > Cyril
> >
> > Rilei Yu a crit :
> > > Dear amber users,
> > > I came across a problem: when I transform the mol2 format file
> > to the
> > > pdb format file in sybyl, the type of a "N" atom also change
> > from the
> > > Nam to the N2 (The only one N atom in the ligand molecule). Then
> > I try
> > > to change the type of the N in the Sybyl to obtain the original
> type
> > > (Nam), unfortunately, I failed.
> > > Questions: Is there any software for me to change the format of the
> > > file from the mol2 to the pdb without the errors appearance?
> > > Is there any way form me to change the atom type of the N and
> > > successfully save it?
> > > I have attached the pdb file to this email. I hope you can help
> > me to
> > > solve this problem and your help will be greatly appreciated.
> > > Best regards,
> > > Rilei Yu
> > >
> > >
> > > Rilei Yu
> > >
> > >
> >
> ------------------------------------------------------------------------
> > > Ż䣬䣡
> >
> >
> >
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> >
> >
> >
> > Rilei Yu
> >
> > ------------------------------------------------------------------------
> > Ż䣬䣡 <http://cn.mail.yahoo.com/>
>
>
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