Re: [AMBER] Parmed.py deletedihedral

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Wed, 24 Jul 2013 13:09:45 +0000

Thank you very much for your help!

-----Original Message-----
From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On Behalf Of Jason Swails
Sent: 24 July 2013 13:16
To: AMBER Mailing List
Subject: Re: [AMBER] Parmed.py deletedihedral

I think I have this issue fixed. As a temporary workaround, though, you can change the mass of the hydrogens you tricked your prmtop into thinking it was gadolinium to something like 14, delete the dihedrals you want deleted, then change the mass back. So something like this:

change MASS .%dh,mh 14
deleteDihedral .33 @32 @36 @37
change MASS .%dh,mh 1.01

HTH,
Jason


On Tue, Jul 23, 2013 at 1:03 PM, Jason Swails <jason.swails.gmail.com>wrote:

>
>
>
> On Tue, Jul 23, 2013 at 10:52 AM, Aronica, Pietro <
> pietro.aronica07.imperial.ac.uk> wrote:
>
>> Thank you for your reply.
>> Yes, I am aware of the fact that VdW parameters are 0. I guess you
>> could call it a prmtop-based FEP scheme, that's not a bad approximation.
>> As for the hydrogens being in the "wrong" list, this is deliberate.
>> We were having problems with SHAKE interfering with our custom atoms,
>> so we needed those bonds to not be considered as including hydrogens.
>> This was accomplished by setting the element of the custom hydrogens
>> to gadolinium (hence the atomic number of 64), though their mass and
>> other parameters are then set to those of a normal hydrogen. The
>> result is that the atoms are effectively hydrogens but are not
>> thought of as such when writing the prmtop. Perhaps bad practice, but
>> as a workaround it works well enough for the moment.
>> Is putting them in the "DIHEDRALS INCLUDING HYDROGEN" list the only
>> solution?
>>
>
> Ah, I see. I guess ParmEd should be a bit more permissive here. This
> code was actually written before the ATOMIC_NUMBER section was added
> to the topology file -- as a result the 'element' is always assigned
> based on the atomic mass in this particular action. A more flexible
> approach would be to look at the mass only if an ATOMIC_NUMBER section does not exist...
> This is easy enough to accomplish.
>
> As an aside, did the "noshakemask" variable not work? In any case,
> this is an improvement worth making.
>
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>



--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jul 24 2013 - 06:30:03 PDT
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