Hi, all, Now, I have made some progress. According to charles' suggestion, I split the seq string into two parts and then start PDBTool after two steps of import psfGen with appropriate startResid. It looks right and I finally get the output of pdb and psf. However, I notice there are some error reports which happen during the script running. I list some of them as following:
"PARRDR-ERROR: duplication of nonbonded entry CS2", or, "PARRDR-ERROR: duplication of bond entry C3S8 HA", or, "PARRDR-ERROR: duplication of angle C3S6 CSN2 C3S7" I check the output pdb file and find that the rotatable bonds between cysteine and the ring of MTSL are missing in the final structure. Is this related to the above error reports? Maybe not, because it seems these bonds are missing as well in the demo output. Since I don't want to go back again to correct my mistakes, here I have another question, that is "whether is this structure without the bond linking between cys and MTSL useful for further ensemble calculation or back calculation?" Thanks for everybody in advance! bwu -----Original Message----- From: Sent: None To: Wu, Bainan Subject: Re: [Xplor-nih] how to incorporate into MTSL into a protein? . . In-reply-to: <5CB39BCA5724F349BCB748675C6CA1A20381957F@SJMEMXMB02.stjude.sjcrh.local> References: <5CB39BCA5724F349BCB748675C6CA1A20381957F@SJMEMXMB02.stjude.sjcrh.local> Comments: In-reply-to "Wu, Bainan" <[email protected]> message dated "Mon, 30 Jan 2006 22:49:00 -0600." X-Mailer: MH-E 7.85; nmh 1.1; GNU Emacs 21.4.1 From: [email protected] Date: Tue, 31 Jan 2006 09:48:12 -0500 Message-Id: <[email protected]> Cc: [email protected] X-BeenThere: [email protected] X-Mailman-Version: 2.1.5 Precedence: list List-Id: xplor-NIH help list <xplor-nih.nmr.cit.nih.gov> List-Unsubscribe: <http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih>, <mailto:[email protected]?subject=unsubscribe> List-Archive: <http://cake.cit.nih.gov/pipermail/xplor-nih> List-Post: <mailto:[email protected]> List-Help: <mailto:[email protected]?subject=help> List-Subscribe: <http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih>, <mailto:[email protected]?subject=subscribe> Sender: [email protected] Errors-To: [email protected] Return-Path: [email protected] X-OriginalArrivalTime: 31 Jan 2006 14:48:27.0800 (UTC) FILETIME=[653A8180:01C62675] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi-- > > I go back to check my pdb file and then find possible mistakes. > The initial structure uses two long linkers to connect three chains. > When I prepare my pdb file, I delete these linkers without giving the > different chain number. This may be the point. > sounds like you're making progress... > Here, I have another question. If there is a jump on residue number due > to the chain break, can addAtom.py read through sequence file to match > the corresponding atoms in pdb file? > For this, modify the addAtoms.py script as follows: 1) split the seq string into two, named say seq1 and seq2, broken at the chain break. 2) call psfGen.seqToPSF twice: first using seq1 and startResid=1 second using seq2 and the appropriate startResid hope this helps-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8 <http://mailcrypt.sourceforge.net/> iD8DBQFD33isPK2zrJwS/lYRArd9AKCBihN3JIDgAHD9eklexpguOtn8sACdEo5t 1fITcR12jVfZfEmhrd2JPhg= =Qc98 -----END PGP SIGNATURE----- _______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
