Dmitrv,
Okay, please set inp=1 in the &cntrl namelist to recover the original
behavior in Amber11. It is also what you intended in the input file,
i.e. using the classical SA model for nonpolar solvation treatment.
The default setting in Amber12 is for inp=2 to use the new way to
compute nonpolar solvation free energy. This method has not been
turned on for nonnatural amino acids or metal ions.
All the best,
Ray
On Wed, Nov 14, 2012 at 9:17 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Dmitry,
>
> It looks like that the input file is asking for radii to be read from the
> prmtop file, so I don't know why the error message got printed. Can you
> email me off the list the prmtop and a sample inpcrd file for us to
> reproduce the problem? I suppose this is from the python script that calls
> sander?
>
> Ray
>
> On Wed, Nov 14, 2012 at 10:21 AM, Dmitry Mukha <dvmukha.gmail.com> wrote:
>>
>> Hi Ray,
>>
>> an input file was following
>>
>> File generated by MMPBSA.py
>> &cntrl
>> ntb=0, igb=10, cut=999.0, nsnb=99999,
>> imin=1, maxcyc=0, cutcap=-1, xcap=0,
>> ycap=0, zcap=0, idecomp=0, ntpr=1,
>> ivcap=0, ntmin=2,
>> /
>> &pb
>> dbfopt=1, epsin=1, epsout=80, istrng=150.0,
>> radiopt=0, sprob=1.4, space=0.5, maxitn=1000,
>> npopt=1, cavity_surften=0.00542, cavity_offset=-1.008,
>> fillratio=4,
>> /
>>
>> Any your suggestions?
>>
>> Best regards,
>>
>> Dmitry
>>
>>
>> 2012/11/14 Ray Luo, Ph.D. <ray.luo.uci.edu>
>>
>> > What's the input file generated for pb calculations?
>> >
>> > Ray
>> >
>> > On Wed, Nov 14, 2012 at 12:52 AM, Dmitry Mukha <dvmukha.gmail.com>
>> > wrote:
>> >
>> > > Hi all,
>> > >
>> > > Amber 12 PB routine doesn't work with FE atom-containing molecules.
>> > > But
>> > > Amber 11 works. I use .in-files created by MMPBSA.py in both versions:
>> > the
>> > > older one works, the output of 12th version contains a line
>> > >
>> > > PB Bomb in pb_aaradi(): No radius assigned for atom 8857 FE FE
>> > >
>> > > Best regards,
>> > >
>> > > Dmitry Mukha
>> > > Institute of Bioorganic Chemistry,
>> > > National Academy of Sciences of Belarus
>> > > Kuprevich Street, 5/2, 220141, Minsk
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>> > >
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Received on Fri Nov 16 2012 - 16:00:01 PST
