[gmx-users] CHARMM36 sucrose?

[Justin Lemkul]

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

==================================================