Hello, I have been having trouble with files in xleap.
I solvated and ionized an amyloid beta fibril in VMD, and then used the charmmlipid2amber.x script to reformat the pdb file for amber (I deleted the 'if' statement that gives and error if the molecule is not a lipid).
When I try to load my pdb file into xleap, it loads correctly, and looks good when I edit it, but I get the following message upon loading it:
Leap added 1299 missing atoms according to residue templates:
55 Heavy
1244 H / lone pairs
The file contained 1962 atoms not in residue templates
When I check the file I get a bunch of FATAL messages saying that "ATOM _____ does not have a type." Almost 2000 of these in fact....
I also get 3550 warnings that say "WARNING: close contact of ________ Angstroms between _______________"
Any ideas what is wrong or what I need to do to fix this?
Just to run a sort of control, I decided to run the RCSB PDB file, without VMD modifications. I get this message:
Leap added 54 missing atoms according to residue templates:
54 H / lone pairs
The file contained 18 atoms not in residue templates
Running the check on this test I get "FATAL: Atom _____ does not have a type." 18 of these
I also get "WARNING: close contact of _____ Angstroms between _________". 57 of these.
This is concerning, because there are a lot of errors and warnings in my simple test of the RCSB file. The grad student I am working with said that for my large solvated/ionized system I should be getting no errors, and only a handful of warnings.
Knowing how to fix this would be great, because I am close to being able to run my MD simulations, but I will not be able to until I know that the PDB file is fixed so that amber can make nice prmtop and inpcrd files.
Thanks in advance!
-Hunter
Hunter Brown
Bassoonist, Contrabassoonist, Composer, Chemical Engineering Major
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Received on Fri Jun 28 2013 - 08:30:02 PDT
