AMBER Archive (2008)

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

From: Cyril Bauvais (
Date: Tue Jun 24 2008 - 09:05:36 CDT

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)...


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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