Thanks for the suggestions.
The reported pmemd.cuda: PMEMD implementation of SANDER, Release 14.
On changing to iat=-1,-1,r1=..., the final disang file looks like this:
Disrance restraint
&rst
iat=-1,-1, r1=0.0, r2=30.0, r3=30.0, r4=35.0, rk2=10.0, rk3=10.0,
IRESID=1,
igr1=111,123,243,172,198, igr2=29,47,62,69,81
/
However, I got following error:
Error: No atom in residue 111
In addition to IRESID=1, do I need to specify atoms using variable ATNAM(1)...ATNAM(8)?
If yes, how to specify ? Or something else is missing here ?
Thanks again,
-- Joshi
________________________________________
From: Marc van der Kamp [marcvanderkamp.gmail.com]
Sent: Friday, December 04, 2015 01:25
To: AMBER Mailing List
Subject: Re: [AMBER] pmemd.cuda with CoM restraints
Also make sure that all the updates to the pmemd.cuda code are applied, and
you have recompiled it.
What version of pmemd.cuda is reported?
--Marc
On 3 December 2015 at 17:22, Charles Lin <clin92.ucsd.edu> wrote:
> Try changing it from iat(3) in your call to just iat=-1,-1,r1=...
>
> I don't believe iat(3) is part of the namelist.
>
> -Charlie
> ________________________________________
> From: Dhananjay (達南杰) [d00b46022.ntu.edu.tw]
> Sent: Thursday, December 03, 2015 6:56 AM
> To: amber.ambermd.org
> Subject: [AMBER] pmemd.cuda with CoM restraints
>
> Dear users,
>
> I successfully run the MD with restraints applied on two atoms (in cpu)
> using disangle specifier as follows:
>
> #Disrance restraint
> &rst
> iat=1220,18, r1=0.0, r2=50.0, r3=50.0, r4=55.0, rk2=10.0, rk3=10.0,
> /
>
> Now, I wish to extend this to protein and a peptide system and want to
> keep them at certain distance by applying distance restraints on centre of
> mass/geometry of two groups of atoms. Therefore, I used igr1 and igr2 as
> follows:
>
> #Disrance restraint
> &rst
> iat(3)=-1,-1, r1=0.0, r2=15.0, r3=15.0, r4=20.0, rk2=10.0, rk3=10.0,
> IRESID=1,
> igr1=1,2,3,4,5,6,7,8,9,10,
> igr2=123,124,125,126,127,128,129,130,131,132,133,134,135,136,
> /
>
> I used pmemd.cuda(GPU) and got following error:
>
> CUDA (GPU): Implementation does not currently support the use of COM
> simulations for angle or dihedral restraints.
> Require iat(3) >= 0.
>
>
> I do not want to apply angle or dihedral restraints but distance only.
> What is wrong here ?
> Any help in this regard will be appreciated !!
> Thanks in advance,
>
>
> -- Joshi
>
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Received on Thu Dec 03 2015 - 20:30:03 PST
