AMBER Archive (2008)

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

From: Junmei Wang (
Date: Tue Jun 24 2008 - 08:47:24 CDT

Did you use antechamber to do the conversion? I found your ligand has no
hydrogen atoms at all, did you add them in sybyl?. If you added hydrogen in
sybyl, you need to double check atom types since sybyl is a bad program to
judge atom types and bond types when only connectivity table is provided
(such as pdb format). There is a funny bug in sybyl handling amide
functional group: it always put double bond between C and N. To correct
this, one needs to modify not only bond type but also atom type (if only
bond type is corrected, only one hydrogen is added when you run add hydrogen

After correcting the atom type and bond type and adding hydrogen, I
correctly assign atom types (both amber and sybyl) from either pdb and mol2.



On Mon, Jun 23, 2008 at 8:01 PM, Rilei Yu <> wrote:

> 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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