You can discard my previous email as I thought you had issues with
creating prmtop/inpcrd files. It seems that you indeed can create those
files, so you do not have any issue with prmtop/inpcrd files (except the
box info if you did not explicitly stated it).
> I have linked leaprc.ff14SB as my default leaprc. I understand this is
> recommended usage?
If you are going to study a protein system, then ff14SB is the latest
force field to use. So, your best bet is with this ff.
Just a side note: If you have nucleic acids in your systems, you need to
be careful in choosing which ff to use.
> I also tried sourcing the frcmod file directly before. Did not seem to make
> any difference.
Attach the leap.log file but it seems that you do not have any issue with
creating prmtop/inpcrd files. If you are going to use ntb=1, this means
that you have periodic box conditions. Did you specify this while creating
the prmtop/inpcrd files? When you solvate the system with water molecules,
this info is automatically loaded. In order to explicitly impose a box to
a system, use 'setbox' command in leap such as 'setbox mol vdw'.
> I do not understand what 'set default PBradii mbondi2' is all about. Is
> this absolutely necessary? If so, why?
Read the manual; this is not a must. It is automatically putting the
mbondi2 radii in the prmtop file in case someone wants to do implicit
solvent MD. I copy/pasted directly from one of my work, so you can discard
it.
> I hope to add solvent (sovateoct 1vom TIP3PBOX 8.0) in the next step but I
> think I should be able to run a protein+ion minimization in vacuum to begin
> with.
Yes you can, but again, it will not mean anything. After you created the
prmtop/inpcrd files, check out the last line in inpcrd. If it does not
have the box info present, you cannot use ntb=1 but ntb=0.
Ilyas,
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Received on Tue May 13 2014 - 14:00:08 PDT
