It looks like you need to define grnam for each of your residues. See page 449 of the amber 15 manual for details and page 468 for an example.
I believe IRESID=1 allows you to choose the residues in which you'll be selecting atoms from then you use grnam to put the atom name from the residue you wish to select for the center of mass. (Ex. grnam1 (1)='C1'). Or you can just use IRESID=0 and select the individual atoms you wish to apply the center of mass restraint to.
Also I believe there were some GPU patches for CoM in update.13 of Amber 14 (pmemd / cuda). Please run $AMBERHOME/update_amber --version to check if you have those updates.
-Charlie
________________________________________
From: Dhananjay (達南杰) [d00b46022.ntu.edu.tw]
Sent: Thursday, December 03, 2015 8:09 PM
To: AMBER Mailing List
Subject: Re: [AMBER] pmemd.cuda with CoM restraints
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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 03 2015 - 23:00:03 PST
