From: Kamp, Marc vander (Marc.vanderKamp_at_wur.nl)
Date: Mon Jun 21 2004 - 07:33:11 CDT
Dear all / VMD-developers,
I am using amber-type parameters in namd. I create the AMBER format input files using the tleap-program (which is included in the NAB-distribution available from the Case-group).
The parmtop file can be read in into VMD without a problem (if you use the parm7 extension the file is automatically recognised) but reading in the crd file as was created by tleap doesn't go well; VMD reads the number of atoms as the first coordinate. This can simply be solved by deleting the first empty line of the crd-file (which makes the number of atoms the first line).
However, if you want to use the crd file as input coordinates in NAMD (using 'ambercoor'), the first line must be empty again (otherwise the coordinates are not correctly understood, leading to 'infinite' energies in minimization).
Of course this is not a very urgent problem, but it would be nice if NAMD and VMD would treat crd files equally. As NAMD can directly use the crd-files that are created with AMBER-suite programs, it would in my opinion be best to change the crd-reading possibility in VMD.
Best to you all,
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