Thank your for your valuable suggesion.
Sorry,I forgot to mention that in addition to the HEATATOMs I also removed the tRNA and ATP to modify the PDB. However as per your suggesion now first I will try to load the same pdb taking only first five residues and I will inform you.
For your kind information, I also tried the same process for the 6PTI.pdb as mentioned in the basic tutorial of amber manual. I also face the same problem. I think I am doing something wrong in any step. But I can not find it out. So, if you kindly inform me all steps how to edit pdb, it will be very helpful for me.
One interesting point when I am generating the pdb file using the same topology file and coordinate file it is not showing the same large bonds. I can not understand what colud be the possible reason?
With my best regards
Sindrila
From: David A. Case <case.biomaps.rutgers.edu>
To: Sindrila Dutta banik <sindrila.duttabanik.yahoo.com>
Sent: Wednesday, 25 May 2011 10:09 PM
Subject: Re: [AMBER] PROBLEM IN TERMINAL RESIDUES: WRONG BONDS
On Wed, May 25, 2011, Sindrila Dutta banik wrote:
>
> The PDB code of the corresponding pdb file is 1AZS.pdb
This is a very large and difficult pdb file: you should expect to spend a fair
amount of time getting this system prepared for Amber.
> The 1ASZ_1.pdb is the modified pdb file. I removed all HETATOM from the
> original pdb file (1ASZ.pdb).
This won't work: by removing HETATM cards, you are removing a large number
of unusual nucleic acid residues, leaving a gap that LEaP will think are
covalently connected.
As far as the protein part goes, you should try loading just individual
chains (or parts of chains) to see if you can identify the problems. I
tried loading the first four residues of the first protein chain, and
everything looked fine. Try this, and other experiments, building up
to larger pieces of the original PDB file until you can localize the
problems. Pay very close attention to all the leap comments and messages.
You will probably need several cycles of editing the pdb and loading into
LEaP until you are able to identify all the problems.
Unless you are an experienced Amberite, I'd suggest you first run some
simulations of the tRNA by itself, and of one of the protein chains by itself.
Make sure you can get stable simulations and know how to analyze them. Then
you can tackle the whole complex (presumably including the ATP as well.)
....dac
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Received on Wed May 25 2011 - 09:30:07 PDT
