VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Tue Nov 11 2008 - 13:23:33 CST

Or perhaps you would like to adapt the membrane builder tool in order to
deal with your membrane. In that way you will be able to obtain a
membrane of any size.

Peter Freddolino escribió:
> Autopsf should take care of the split/recombine process automatically,
> although you'll want to verify that the results are reasonable. You
> can get at it via the command line or GUI (under Modeling).
> Best,
> Peter
>
> Edward Lyman wrote:
>> Dear all,
>>
>> I have a pdb and a psf for a membrane system, and I want to build a
>> system that is twice as big, by shifting the coordinates by the box
>> dimension in y. shifting the coordinates and writing them to a pdb is
>> simple enough, but I am trying to find a simple way to generate a
>> combined pdb/psf for the whole, doubled system. if i try to read the
>> psf and the first pdb, then re-read the psf and read the second pdb,
>> I get an error "Unable to add (duplicate?) residue C001:1". but, even
>> if I am able to do so, I think I might have too many residues per
>> segment.
>>
>> In the past, I dealt with this by painstakingly splitting the pdb's
>> into separate segments, renaming segments until I had enough,
>> regenerating the psf's, and then sticking it all back together with a
>> series of readpsf/readpdb's, then writing everything. But I think
>> there must be a cleaner, faster, less annoying way...
>>
>> Thx,
>> E
>>
>