AMBER Archive (2008)

Subject: Re: AMBER: Further request answers from Dr. Junmei Wang

From: Junmei Wang (junmwang_at_gmail.com)
Date: Tue Jun 24 2008 - 11:58:49 CDT


Hi, Rilei,
In fact, antechamber only requires correct connectivity to function well. I
usually use sybyl to add hydrogen atoms. As I mentioned in the last email,
to correct add hydrogen, you need to make sure the atom types and bond types
are correct. Otherwise more or fewer hydrogen atoms are wrongly added.

When you read in a pdb file in sybyl, for the amide group in the
non-standard residues, you need manually modifiy bond type of C-N from 2 to
1 and atom type of N from N2 to Nam. After that, you fill in the open
valences with "add hydrogen" in the "Build" pulldown menu. It is recommanded
to save the ligand in mol2 format and use it to generate prepi files.

Best

Junmei

2008/6/24 Rilei Yu <yulaomao1983_at_yahoo.com.cn>:

> Dear Dr. Junmei Wang,
>
> I believe your answers is very feasible to solve my problem-tranform the
> mol2 file to the pdb file. However, when I modified both the atom type and
> bond type of the N atom and saved it in Sybyl, the information could still
> not be saved in the new pdb file. Could you tell me, what kind of software
> do you use to modify the N atom? Or do you directly modify it in the pdb
> file? When I open the pdb file, I could hardly found the information to rule
> the atom type of the N atom.
> (HETATM 60 N M_ 1 3.080 -8.424 9.737 1.00 -0.22 )
>
> I hope you can further provide me answers to solve my questions. Thanks for
> your help again!
>
>
>
> ** **
> **
> **
> **
> *Junmei Wang <junmwang_at_gmail.com>* д
>
> Hi
> 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
> command).
>
> 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.
>
> Best
>
> Junmei
>
>
> On Mon, Jun 23, 2008 at 8:01 PM, Rilei Yu <yulaomao1983_at_yahoo.com.cn>
> 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 <http://cn.mail.yahoo.com/>
>
>
>
>
>
> Rilei Yu
>
> ------------------------------
> Ż䣬䣡 <http://cn.mail.yahoo.com/>
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