[gmx-users] Build oligosaccharide topology with pdb2gmx

[Elena Lilkova]

Hi,

unfortunately, my idea does not work. When I define the sugars in the
residuetypes.dat as "Other" it does not patch the termini, and pdb2gmx
says:

Warning: Starting residue SGN1 in chain not identified as Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.

If I declare them to be protein, it tries to patch them, but complains that:

Atom O in residue SGN 1 was not found in rtp entry SGN with 28 atoms
while sorting atoms.

So, I'll just do the big single rtp entry for the whole thing.

Thanks anyway and have a nice evening,

Elena

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