VMD-L Mailing List
From: Sanjeev B.S. (sanjeev_at_mbu.iisc.ernet.in)
Date: Wed Oct 30 2002 - 07:50:45 CST
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- In reply to: Vlad Cojocaru: "carnal output trajectory"
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I could not do a single step carnal, so settled with two step. Later I
used ptraj to do the task. The example in ptraj does not work, 'cos the
sequence of the commands are upside down! the following is the one that I
presently use to do the job to generate PDBs fitted with a reference
structure and the molecule placed at center of the box. Hope this helps.
--- reference /home/sanjeev/MD/1HI2/INPUT-MINIM/molecule.min.crd trajin /home/sanjeev/MD/1HI2/CRD/molecule.0000_0010.crd.gz trajin /home/sanjeev/MD/1HI2/CRD/molecule.6370_6380.crd.gz trajin /home/sanjeev/MD/1HI2/CRD/molecule.6380_6390.crd.gz trajin /home/sanjeev/MD/1HI2/CRD/molecule.6390_6400.crd.gz trajout molecule.pdb PDB center @CA image rms reference out CAmolecule.rms @CA go --- On Wed, 30 Oct 2002, Vlad Cojocaru wrote: Dear Amber users, I found out that OUTPUT COORD option in carnal has an option BOX which is not written in the manual. With this option I managed to output trajectories in a proper way for visualizing them with VMD. Now the question is that I want to see the trajectory after fitting all the structures to the first frame. The BOX option seems not to work anymore when I give to carnal the following: DECLARE GROUP g1 (RES 1-17); IMAGE img g1%cmass; RMS fit1 FIT g1; OUTPUT COORD crd fit1 BOX; The program gives an error message that tells me that the BOX option does not work with fit. If I do not use the BOX option the trajectories are again impossible to visualize with VMD. Does anyone have any suggestions about this?? Thanks a lot! vlad
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- In reply to: Vlad Cojocaru: "carnal output trajectory"
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