VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Apr 19 2016 - 19:33:32 CDT

So I haven't tested anything yet, but a skimming of the files you sent over
shows that the PDB you start of with (not sure if that is included or not)
is probably not correct.

Usually when you have multiple chains you should have a "TER" flag
separating one chain from the next. I am guessing you were either missing
this or something else. The reason why I say this is that your PSF shows a
BOND between your chain A and Chain B --- atom 1413 connected to 1415 --
line 84040 of the PSF file. This should not happen since the chains are not
covalantly linked -- if they were it would be one giant protein.

Look into this "TER" separation of PDB so as to ensure that the chains are
not bonded in the PSF. I am not sure if this will solve the solvation
problem or not - but it might -- will test in detail shortly and see if I
can find a fix.

Best,
/A
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