I don't know enough about docking to say whether it will work. For MD,
I don't know a better solution than using a full protein instead of a
piece of it. Sorry! Maybe there are examples in the literature?
Leap renumbers the residues as it reads them such that the first
residue is 1, the second is 2, and so on. If the residues in the PDB
are not numbered sequentially starting from 1 they will be different
from leap's numbers. So perhaps as a result you've put the TER records
in the wrong places?
There is also a leap command to remove these bonds after you've loaded
the PDB (see the manual).
--Tom
On Fri, Jul 31, 2009 at 9:38 PM, Qinghua Liao<fantasticqhl.yahoo.com> wrote:
> Hi Tom,
>
> Thanks for your reply! If I just want to do docking, it is ok, is that right? Or if I want to do MD, how should I add those missing residues? By the way, I follow your suggestion to insert TER between those residues, there are still the same warnings when loaded in xleap. What's the matter? Thanks!
>
> Qinghua
>
>
>
>
> ________________________________
> From: Tom Joseph <ttjoseph.gmail.com>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Saturday, August 1, 2009 12:41:49 AM
> Subject: Re: [AMBER] problem from xleap
>
> I only looked briefly but this does not look like a complete protein.
> Many residues are missing, which leaves many regions unconnected.
> Please be sure this is OK for what you want to do (e.g. for MD, the
> resulting simulation may be quite different from how the receptor acts
> in reality). You may wish to use a complete protein without gaps.
>
> Leap joins together residues that are adjacent in the PDB file, even
> if the bond length would be unrealistic. You can keep it from doing
> this by inserting TER records in the PDB file between the residues
> that need to be separated.
>
> --Tom
>
> On Fri, Jul 31, 2009 at 10:38 AM, Qinghua Liao<fantasticqhl.yahoo.com> wrote:
>> Dear amber users,
>>
>>
>> I have a problem when using xleap. when I load the pdb file of receptor, then check it, it gives me those warnings that there are several bonds with a more than 10 angstroms bond length. The attachment file is the pdb file of receptor for you to check for me!
>>
>> I can't understand that. Could somebody tell me the reason? Any response will be highly appreciated!
>>
>> All the best!
>>
>> Qinghua
>>
>>
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Wed Aug 19 2009 - 20:03:09 PDT
