[gmx-users] adding SR2++ to charm27 force field

Ming Tang m21.tang at qut.edu.au
Wed Apr 15 05:38:02 CEST 2015

Dear Justin and mark,

I modified the files like this:


[ MG ]
 [ atoms ]
	MG	MG	2.00	0
[ SR ]
 [ atoms ]
	SR	SR	2.00	0


[ moleculetype ]
; molname   nrexcl
MG          1

[ atoms ]
; id    at type     res nr  residu name at name  cg nr  charge
1       MG          1       MG          MG       1      2  
[ moleculetype ]
; molname   nrexcl
SR          1

[ atoms ]
; id    at type     res nr  residu name at name  cg nr  charge
1       SR         1       SR          SR       1      2    


CP1	MG	1	0.274842254546	0.051243325419
CP1     SR      1       0.310269        0.494658 
whenever there is MG, I add SR.


CN7	MG	1	0.274842254546	0.051243325419
CN7     SR      1       0.310269        0.494658
whenever there is MG, I add SR.	   


MG	24.305000 ;	Magnesium Ion 
SR          87.62000  ;           Strontium Ion

When I copy the modified force field to the working directory,  the PDB file used to consider MG Cannot be minimised too, which works well with the original Charmm27 force field. It reminds that atomtype SR not found again.
I use ready-made pdb file and topol file for minimization.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, 15 April 2015 1:22 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] adding SR2++ to charm27 force field

On 4/14/15 5:12 AM, Ming Tang wrote:
> Hi Mark,
> Thanks for your reply. I am sure as I changed the files in the charmm27.ff installed in my unbuntu system. Is there any other things I need to consider?

The files you listed are the only ones that should need to be modified.  Either you missed a step and think you did something you didn't, or your changes didn't actually take effect (modifying the top-level installation usually requires admin privileges, so if you tried to modify without sudo or root it won't take). 
  Experiment with a local copy of the directory rather than potentially messing up something system-wide.  The error points most likely to the .atp file.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul

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