[gmx-users] CHARMM36 sucrose?

[Smith, Micholas D.]

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)

-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 8:40 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] CHARMM36 sucrose?

On 8/19/14, 8:29 PM, Smith, Micholas D. wrote:
> Hi gmx_users,
>
>
> I am trying to run a simulation that includes a sucrose molecule constructed with the CHARMM36 AGLC and BFRU carbohydrate residues. The problem is when I run pbd2gmx with the system, the sucrose molecule splits into a separate glucose and fructose molecules, as if it is splitting a chain. It looks like the is that the residues aren't being recognized as chain molecules with the following warnings:
>
>
> Warning: Warning: Starting residue AGLC0 in chain not identified as Protein/RNA/DNA.
>
> Warning: Starting residue BFRU0 in chain not identified as Protein/RNA/DNA.
>
>
>
> Any known solution to this? I've seen that it might be possible to copy-paste the two units together and make a new residue, but this seems like it might be the wrong direction.
>

Does the topology get written, and if so, are the proper bonded interactions
assigned?

The warnings are not actually important.  The only valid types in
residuetypes.dat are Protein, DNA, RNA, Ion, and Water.  Anything else gets
lumped into "Other," which is only really significant if you've got some custom
residue in the middle of a biopolymer with a different type.

The other thing that you might need to consider is that both your AGLC and BFRU
have the same residue index (zero), so any bonded interactions in the .rtp that
use the +/- mechanism probably won't work.

-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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