you say you want to use ff02 but then say you can't find leaprc.ff12 ...
are you looking for leaprc.ff02?
also you seem to be loading leaprc.gaff, but GAFF is not a polarizable
force field. I think you need to decide if you're trying to use a
polarizable model or not, mixing all of these different types of models
might not work well (if it works at all).
I suggest looking earlier in your leap log and follow all of the messages.
If it was not able to load the protein force field, you will get errors
later but the real problem is making sure the libraries were properly
loaded.
On Thu, Aug 3, 2017 at 11:15 PM, Aishwarya Venkatramani <avenkatr.ucsd.edu>
wrote:
> I am having an issue with using ff02 (polarizable force field) to set up a
> simulation using tleap.
>
> When I look under /opt/amber/dat/leap/cmd I don't see leaprc.ff12 in
> AMBER14 which according to the manual should be there.
>
> Here is my script:
>
> source leaprc.ff02
>
> source leaprc.gaff
>
>
> loadamberparams frcmod.ionsjc_tip3p
>
> loadamberparams frcmod.ionslm_1264_tip3p
>
> loadamberparams frcmod.ff02pol.r1
>
>
> set default IPOL 1
>
>
> mol = loadpdb 4Ca_CaM_pqr.pdb
>
> solvateBox mol TIP3PBOX 12 ....
>
>
> This is the error I get:
>
> ....... FATAL: Atom .R<ALA 147>.A<O 10> does not have a type.
>
> FATAL: Atom .R<ALA 147>.A<OXT 11> does not have a type.
>
> Failed to generate parameters
>
> Parameter file was not saved.
>
>
>
>
> When I use "source leaprc.ff14SB" instead of leaprc.ff02 the script works
> fine,
>
> but would it be okay to use a non polarizable force field and load
> parameters for
>
> a polarizable force field?
>
>
> Any advice would be much appreciated.
>
>
> Thank you,
>
> Aishwarya Venkatramani
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 04 2017 - 06:00:06 PDT
