From: Jason Richard Mick (dw2413_at_wayne.edu)
Date: Sat Aug 14 2010 - 08:37:31 CDT
You should look at how patch residues (PRES) are applied to serine and other amino acid residues in the latest version of CHARMM. A patch lets you add a small modification on to amino acids (see phosphorylated serine, for example). This would be the easiest and most efficient route to accomplish what you are asking.
As for the Asn residue, that's a bit more challenging. What you will likely have to do is figure out how much space the Asn is going to occupy and then shift the coordinates of the previous residues accordingly, inserting the new residue in your PDB file, while making sure your R-chain isn't overlapping the rest of residues. Molecular modelling tools like Gaussian View (if you have access to it) may even allow you to directly do this, without even editing the PDB file by hand or by script.
From: "Aditya Ranganathan" <aditya.sia_at_gmail.com>
To: namd_at_ks.uiuc.edu, "NAMD list" <namd-l_at_ks.uiuc.edu>
Sent: Saturday, August 14, 2010 6:57:28 AM
Subject: namd-l: Modifying a peptide and introducing residues
I`m at the moment looking at starting a simulation with somatostatin which is 14-residues long and has the following sequence:. Ala-Gly-Cys-Lys-Asn-Phe-Phe-Trp-Lys-Thr-Phe-Thr-Ser-Cys.
However, the only coordinates available on PDB and structures resolved are of synthetic constructs of somatostatin analogues which have modified residues or nontypical residues. Is there a method by which I could change those non-typical residues like D-TRYPTOPHAN or 3-IODO-TYROSINE or 4-[(ISOPROPYLAMINO)METHYL]PHENYLALANINE to the ones which are present in the actual peptide.
Also, the coordinates of analogue structure in PDB does not have the Asn residue which is present in somatostatin peptide at the 5th position between the Lys and Phe residues.
Is there a way I could add the missing residue to the available PDB file? I would also like to notify that the peptide forms a ring like structure or cyclic structure between the Cys at the 3rd position and Cys at the last position.
Please help me out with this as I need it urgently as a part of my project.
Junior Research Assistant and Masters Student,
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