AMBER Archive (2008)

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

From: Rilei Yu (yulaomao1983_at_yahoo.com.cn)
Date: Tue Jun 24 2008 - 11:14:15 CDT

 
  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

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo_at_scripps.edu

Rilei Yu
       
---------------------------------
 ÑÅ»¢ÓÊÏ䣬ÄúµÄÖÕÉúÓÊÏ䣡
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu