[gmx-users] Build oligosaccharide topology with pdb2gmx

[Justin Lemkul]

On 3/4/15 9:03 AM, Elena Lilkova wrote:
> 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.
>

Worth a shot.  Please report back if this works; it would be very useful to know 
and would be a nice benefit for the community.

-Justin

> 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
>>
>> ==================================================
>>
>

-- 
==================================================

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

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