Hello sir,
I am working on free energy calculation for protein systems using
MMPBSA.py in ambertools.
While running MMPBSA.py for my systems I was struck with a doubt
regarding saltcon in mmpbsa.in(script).
My systems contain:CA+,MG+,I-,SOD+ ions .
I had gone through the ambertools mailing list.were I got few links
(mentioned below).
http://archive.ambermd.org/201104/0284.html
http://archive.ambermd.org/201101/0612.html
Also i have gone through the paper related to salt strength which is
referred in ambertools14.
ref:121
http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.208.7194
which cleared some of my doubts like including explicit ions in an
MM/PBSA calculation.
bt I have few more which I like to know from you.
1) After going through amber manual I came across "kappa" keyword
k=(0.10806I)1/2,where "I" is ionic strength which is in [M].
is this keyword anyway helpful in calculating saltcon for my system.
2) In the paper they discussed about salt contribution in GB
theory,but I didn't get any of the formula related to saltconc
calculation.
Thanks in advance
Regards
Vijay
On Fri, Mar 6, 2015 at 10:26 PM, vijay kumar narsapuram <
nvijay1991.gmail.com> wrote:
> WOW...!! its working...Thank you jason.swails
>
> Regards
> Vijay
>
> On Fri, Mar 6, 2015 at 8:58 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Fri, Mar 6, 2015 at 10:22 AM, vijay kumar narsapuram <
>> nvijay1991.gmail.com> wrote:
>>
>> > I used following commands,then i got some ERROR which i am unable to
>> trace
>> > out..
>> >
>> > -$AMBERHOME/ParmEd-master/parmed.py
>> >
>> > -chamber -top top_all27_prot_na.rtf -top top_all36_cgenff_mod_vj.rtf
>> -param
>> > par_all27_prot_na.prm -param par_all36_cgenff_mod_vj.prm -str
>> > AEE-ligand_hydrogens.str -psf newpsf.psf -crd newpdb.pdb
>> >
>> >
>> > ERROR:
>> > [snip]
>> >
>> > del self.pointers['IPTRES']
>> > KeyError: 'IPTRES'
>> >
>>
>> I basically *just* fixed this (someone reported it to me about 2 days
>> ago). If you update ParmEd and re-run, it should work correctly. (Here is
>> the Pull Request: https://github.com/ParmEd/ParmEd/pull/67)
>>
>> Thanks for the report,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Mar 13 2015 - 02:30:03 PDT
