AMBER Archive (2008)

Subject: AMBER: RE: 回复: AMBER: RE: 回复: AMBER: RE: 回复: AMBER: RE: 回复: RE: AMBER: Disturb you for help !?=

From: Yong Duan (
Date: Wed Jan 16 2008 - 10:13:15 CST

Dear Mr. Yu:
>From what you said below, you were unable to load the ligands into AMBER to
generate prmtop. If this was the case, your prmtop file should not have any
bond information (actually any information at all) of the ligands. I am
still a bit confused how could you ever start a simulation without prmtop or
with a prmtop that does not have the things that you want to study. But,
never mind ... Perhaps, your question should be "I can not generate prmtop
file ...".
If the ligands are just peptides of standard amino acids, you can rename the
atoms and residues to the standard names and save them in PDB format. Then,
Leap will recognize them. Make sure you put "TER" cards before and after the
ligands. If the ligands are made of non-standard amino acids and you made
them in Sybyl, you can save the molecules in mol2 format and use antechamber
to generate the relevant information for the ligands.
Just curious, how much do you know the basic theory about molecular
modeling? If you are a beginner, a good starting point is to read a couple
of books. There are numerous excellent books. Most these books are basic
enough to be used for "bed-time reading". Many found Andrew Leach's book
suitable to beginners. If you really do not have time, read AMBER manual.
Perhaps, you should start from a simple case before you work on this. My
suggestion to you is to follow the tutorials first to learn to build a "new"
-----Original Message-----
From: [] On Behalf Of
捞毛 渔
Sent: Wednesday, January 16, 2008 6:56 AM
Subject: 回复: AMBER: RE: 回复: AMBER: RE: 回复: AMBER: RE: 回复: RE:
AMBER: Disturb you for help !?=

Dear Dr Yong,
Thanks for you quick reply!
The prblems as follows:
But you still have not answered my question, how did you know there is a
bond information in your topology file?
Before docking, there is a bond in the ligand. However, after docking is
carried out, I found the some bonds in the ligand is lacking. So I linked
them manually. But when I carried out md using amber, I found the bonds
disconnected again.
Another problem, when I docked some short peptides into some receptors, I
found these ligands could not be treated as a peptide again. (When I
extrated these ligands and display them the vmd or sybyl. In the
substructure blank, the residues can not be showed. It just consider the
ligand as a hetero-molecular) So it could not be loaded into the amber to
generate the prmtop and inpcrd files directly. It is really a hard work to
solve this problem.
Can you tell me some good way to solve this problem?
Thanks in advance!
Rilei Yu



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