[AMBER] Leap question/suggestion for leap developers

From: Sergio R Aragon <aragons.sfsu.edu>
Date: Sun, 12 Jun 2011 19:23:14 +0000

Dear Amber developers,

Adding residues to a protein whose pdb file shows some to be missing is a typical problem encountered by many researchers studying proteins. While the package "modeller" seems capable of doing this in the general case, many simple cases can be done within leap. These are the cases when the peptides to be added are very short. The situation in leap could be made simpler if there is a way to deal with the following situation. With the sequence command, one can readily add a peptide to either the beginning of the end of a protein segment in a single chain pdb file. However, if the missing peptide is either in the middle of the chain, or there are multiple chains in the pdb file and each chain is missing residues at the beginning or end, then we have a small problem. Giving the proper set mol head or tail commands, one can add
A missing peptide segment in the right place, but leap will apparently always place the added residues at the end of the entire chain, EVEN if one has cleared a segment of the protein by using dummy residues that are removed after the chain is loaded into leap (with clearpdbresmap). The workaround for this case is to add all the peptides and save the file, and then use an editor to move them into the proper sequence position. It seems that this work could be avoided if the leap code would place the added residues in the gap, when the right number of gap positions have been cleared to fit the added residues.

Here is an example: (AMBER TOOLS 1.4)
Test.pdb contains the sequence {LYS LYS XXX XXX PRO VAL}, where XXX are missing residues which were inserted into the original pdb file with no atom descriptors, just as place holders for residues.
Suppose the missing peptide is {SER GLU}. Then in tleap:
>mol=loadpdb test.pdb
>remove mol mol.3
>remove mol mol.4
>pep=sequence {SER GLU}
>set mol tail mol.2.21
>pro= sequence{mol pep}
>desc pro
R<LYS 1>
R<LYS 2>
R<PRO 5>
R<VAL 6>
R<SER 7>
R<GLU 8>

The desired behavior would be that the pep would be interleaved between the LYS and PRO, since
There is space cleared for the residues there. Is there a way to achieve this with leap as is? Is this a simple code fix?



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Received on Sun Jun 12 2011 - 12:30:02 PDT
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