[gmx-users] Build oligosaccharide topology with pdb2gmx

Elena Lilkova elilkova at phys.uni-sofia.bg
Wed Mar 4 15:25:59 CET 2015


Hi, Justin,

thanks for the quick reply.
I was thinking of making each saccharide a separate chain, so that each
saccharide goes through the termini patching. As I understand it, my new
.tdb should be something like:

; Link at C4 of res (i-1) for (i)1->4(i-1) linkage
[ LINK-C4 ]
[ replace ]
C4 C4 CC3161 12.011   0.09
O4 O4 OC301  15.9994 -0.36
[ delete ]
HO4

; Link at C1 of res i for (i)1->4(i-1) linkage
[ LINK-C1 ]
[ replace ]
C1 C1 CC3162 12.011   0.29
[ delete ]
HO1
2O1

And then adding the following to the specbond.dat:
RES1   O4   1   RES2   C1    1    0.14     RES1   RES2.

Anyway, eventually I will probably just create one ginormous "residue" for
the whole ilogosacchiride.

Thanky you once again,

Elena

>
>
> On 3/4/15 7:54 AM, Elena Lilkova wrote:
>> Dear GMX community,
>>
>> I would like to use the CHARMM 36 carbohydrate force field to simulate
>> an
>> oligosaccharide. I read the pdb2gmx section of the manual, but I am
>> still
>> wondering how to build the topology for my oligosaccharide.
>>
>> My first question is can I add in the "residuetypes.dat" residues that
>> are
>> neither protein, nor DNA, RNA, water, or ions, but say type sugar.
>>
>
> Listing it simply as "Other" is the straightforward solution.
>
>> Next, how can I link the individual saccharides. I would like to use two
>> of the several linkages, that are parameterized in the force field (i.e.
>> PRES 14aa and PRES 14ab). This means that in both of the two consecutive
>> saccharides some atoms should be deleted and some partial charges should
>> be changed.
>> I now how to do this with the psfgen plugin of vmd, but how am I
>> supposed
>> to achieve this with pdb2gmx. I should probably make a termini database
>> file and a special bonds file, right?
>>
>
> No, the .tdb will only affect the terminal residues and won't do internal
> patching.  At present, there's no built-in way for pdb2gmx to do patching
> like
> CHARMM does.
>
> The possible solutions are:
>
> 1. Write a script to convert the PSF to GROMACS .top format (eventually we
> will
> support PSF natively)
> 2. Create an .rtp entry for the fully built oligosaccharide, with all of
> the
> changes to atom types and charges already made.  The oligo effictively
> becomes
> on single "residue."
>
> -Justin
>
> --
> ==================================================
>
> 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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