Sorry, I mean I am not able to find leaprc.ff02 in AMBER 14 under /opt/amber/dat/lea/cmd.
I also tried using AMBER 16, but ff02 does work (even after removing leaprc.gaff).
This is the error I get:
Could not open file leaprc.ff02: not found
Thank you,
Aishwarya
> On Aug 4, 2017, at 8:40 AM, Carlos Simmerling <carlos.simmerling.gmail.com> wrote:
>
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 04 2017 - 06:00:07 PDT
