Many thanks for the responses.
Jason, do you know what went wrong in using the python script?
[zeus]$ $AMBERHOME/bin/python ChangeParmRadii.py -p peptide.top -r mbondi3 -n peptide3-mbondi3.top
Reading in your topology file peptide.top
Changing radius set to mbondi3
Traceback (most recent call last):
File "ChangeParmRadii.py", line 217, in <module>
mbondi3(parm)
File "ChangeParmRadii.py", line 144, in mbondi3
mbondi2(parm) # start from mbondi2 radii
File "ChangeParmRadii.py", line 114, in mbondi2
molecule = parm.ToMolecule()
File "/cvos/shared/apps/amber/amber11/lib/python2.6/chemistry/amber/readparm.py", line 883, in ToMolecule
if self.valid and self.rst7.valid:
AttributeError: amberParm instance has no attribute 'rst7'
cheers,
Peter
On 7 Sep 2011, at 06:36, Jason Swails wrote:
> On Tue, Sep 6, 2011 at 2:38 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> the manuscript on these is under review. I think Jason's script is ready.
>> mbondi2 radii are ok but mbondi3 are optimized and do indeed give much
>> improved salt bridge strength and other properties.
>>
>
> I had fixed the issues my script had previously (which prevented me from
> including it in the AmberTools 1.5 release). The script was a
> quick-and-dirty solution to changing radii sets and is *only* capable of
> setting intrinsic radii to one of the leap-specific sets (bondi, mbondi,
> mbondi2, amber6) and mbondi3 (as described in the paper Carlos is
> referencing), and I've attached it here.
>
> Quite awhile ago I actually incorporated the functionality found in this
> program (along with all of my other little topology file editing scripts)
> into a single parameter file editor that is vastly more flexible than the
> script I included here which should make many tasks easier (and a couple
> others possible in the first place). This will be included (I think/hope)
> with the next AmberTools release, so I'm just tossing in a little advance
> advertisement here :).
>
> To run the script I attached here, you'll need to have AmberTools 1.5
> installed. This script depends on the chemistry python package directory
> found in $AMBERHOME/AmberTools/src/etc/chemistry. As a result, it's easiest
> if you allow AmberTools 1.5 to build its own version of python. If you do
> this, then you can execute the script included as follows:
>
> $AMBERHOME/bin/python ChangeParmRadii.py --help
>
> That should tell you how to use it.
>
> Hope this helps,
> Jason
>
>
>> On Tue, Sep 6, 2011 at 1:56 PM, Peter Varnai <P.Varnai.sussex.ac.uk>
>> wrote:
>>
>>> Dear All,
>>>
>>> This is to inquire whether there has been any update regarding the mbondi3
>>> parameters for protein simulations with igb=8.
>>>
>>> The amber11 manual states (p. 57) that the mbondi2 radii are fine to use
>>> with igb=8 which Carlos mentioned is the case indeed on 27 April but some
>>> new modifications are available to improve those results for salt bridges.
>>> The manual also details new scaling and atom-specific parameters which all
>>> seems to have been implemented in mdread.f (apparently these can be changed
>>> in the mdin file).
>>>
>>> I would be happy to update the protein atom radii in the prmtop file to the
>>> most recent mbondi3 values: (i) has the paper been published that gives
>>> those values? (ii) Jason's python script may be made available that corrects
>>> for those? (iii) is there a leap fix available?
>>>
>>> Many thanks,
>>> Peter
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Received on Wed Sep 07 2011 - 11:00:02 PDT
