Dear Sindrila,
Providing the list of commands you used in LEaP to generate your
prmtop/prmcrd files (use 'verbosity 2' in LEaP), or providing the
corresponding .log file would help to understand your problem.
regards, Francois
> 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 Thu May 26 2011 - 00:30:02 PDT
