AMBER Archive (2008)

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

From: Cyril Bauvais (bauvais_at_itodys.jussieu.fr)
Date: Wed Jun 25 2008 - 08:00:54 CDT

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>/* дµÀ£º
>
> 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
> >
> >
> ------------------------------------------------------------------------
> > ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡
>
>
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>
>
> Rilei Yu
>
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