[gmx-users] CHARMM36 sucrose?
Smith, Micholas D.
smithmd at ornl.gov
Wed Aug 20 16:49:26 CEST 2014
Just wanted to post a quick update: The psf I had didn't have the linkage in it explicitly (it was relying on the patches we mentioned before). I ended up just swapping over to gromos53a6 instead and using the automated topology builder to run the simulation. I am still going to try to write something to take the psf and make a top with the linkage so I can use the charmm force-field, but that's now a side project.
Thanks again
-Micholas
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Tuesday, August 19, 2014 9:52 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] CHARMM36 sucrose?
On 8/19/14, 9:48 PM, Smith, Micholas D. wrote:
> Thanks for getting back to me.
>
> Any suggestions on tools to build the sucrose residue? At the moment I also have a psf for the composite (as if I was using CHARMM), so I can (in principle) convert the psf to a .top, but curious to see if you or anyone else has a tool for automating the addition of the linkages.
>
No, I don't have anything, though it's something I'm thinking about. If you
already have the .psf, converting it to a .top should be straightforward.
-Justin
> -Micholas
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
> Sent: Tuesday, August 19, 2014 9:10 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] CHARMM36 sucrose?
>
> On 8/19/14, 9:03 PM, Smith, Micholas D. wrote:
>> So the topology file that is written for the sucrose molecule is: [ moleculetype ]
>> ; Name nrexcl
>> Other 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass typeB chargeB massB
>> ; residue 0 AGLC rtp AGLC q 0.0
>> 1 CC3162 01 AGLC C1 1 0.34 12.011 ; qtot 0.34
>> 2 HCA1 01 AGLC H1 2 0.09 1.008 ; qtot 0.43
>> .
>> . (this is filled out correctly)
>> .
>> residue 0 BFRU rtp BFRU q 0.0
>> 25 OC3C51 02 BFRU O5 25 -0.4 15.9994 ; qtot -0.4
>> .
>> . (again, correct here)
>> .
>> 48 HCP1 02 BFRU HO4 48 0.42 1.008 ; qtot 0
>>
>> [ bonds ]
>> ; ai aj funct c0 c1 c2 c3
>> 1 2 1
>> 1 3 1
>> 1 7 1
>> 1 8 1
>> 3 4 1
>> 5 6 1
>> 5 7 1
>> 5 16 1
>> 5 20 1
>> 8 9 1
>> 8 10 1
>> 8 12 1
>> 10 11 1
>> 12 13 1
>> 12 14 1
>> 12 16 1
>> 14 15 1
>> 16 17 1
>> 16 18 1
>> 18 19 1
>> 20 21 1
>> 20 22 1
>> 20 23 1
>> 23 24 1 (!bond joining AGLC and BFRU, seems to be missing...)
>> 25 26 1
>> 25 29 1
>> 26 27 1
>> 26 36 1
>> 26 41 1
>> 27 28 1
>> 27 28 1
>> 29 30 1
>> 29 31 1
>> 29 45 1
>> 31 32 1
>> ... more bonds (these look correct)
>>
>> Pairs also seem fine. It looks like it is something to do with the bonding of the two residues. Is their a way to get gromacs to recognize the chain (the shared linkage/ether bond)
>>
>
> If you're using the default residues included in the force field, no. All of
> the monosaccharides are just that - individual sugars. If you want linkages,
> you have to design your own residues. Gromacs does not have the same patching
> capability that CHARMM has, to modify bonded interactions within the chain.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> 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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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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