[gmx-users] Using CHARMM36 in GROMACS to simulate polysaccharides

[Mohammad Hassan Khatami]

Thanks Justin! It worked. All bonds are now in place.
I’ll play with the branching a bit and will make a new ticket, if I had a problem.
Thank again,
MH
> On May 24, 2017, at 1:04 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 5/24/17 12:04 PM, Mohammad Hassan Khatami wrote:
>> Sorry for that. Here are the types.
>> atom       type
>> C1       CC3162
>> O4       OC311
> 
> O4 should be OC301 for all 1-4 linkages (PRES 14aa, 14ab, 14ba, 14bb in top_all36_carb.rtf).
> 
> -Justin
> 
>> C4       CC3161
>> C5       CC3163
>> C3       CC3161
>> H4       HCA1
>> 
>> I checked them, but I was not able to find the exact combination of atoms angles and dihedrals associated with them in the ffbonded.itp.
>> For example, I did not find C4-O4-2C1 (CC3161  OC311   CC3162) there, but I found both
>> CC3161   CC3162    OC311
>> CC3162   CC3161    OC311
>> 
>>> On May 24, 2017, at 11:39 AM, Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>> wrote:
>>> 
>>> On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote:
>>>> 
>>>>> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami <mhk302 at mun.ca <mailto:mhk302 at mun.ca> <mailto:mhk302 at mun.ca <mailto:mhk302 at mun.ca>>> wrote:
>>>>> 
>>>>> Some how I figured out the problem and fixed it! I changed  "O4   +C1"  to  "O4   2C1” and it worked. I hope it is correct.
>>>> Nope! the bond are not made this time! That’s why grompp did not complain!
>>> 
>>> That's because CHARMM and GROMACS use different syntax.  CHARMM patches use 1 and 2 to denote the first and second residues supplied in the patch call in the input script. You can't do the same thing in GROMACS.  + and - are to specify next and previous residue in the .rtp, respectively.  pdb2gmx will silently accept nonexistent atoms like 2C1 because a +/- designator may exist in a terminal residue, in which case the atom won't be found.
>>> 
>>> Your previous message is also not what I asked for.  I know what the atom names are, and I know what the atom types should be, but I don't know what *types* you actually ended up with in the topology.  Please provide the *types* corresponding to the lines that generate errors.
>>> 
>>>>> Now I have to move on to make the more complicated form of my polymer, and add 1->6 connection to the system, like below:
>>>>> 
>>>>>                           1->6 —AGLC—1->4—AGLC.
>>>>>                         /
>>>>> AGLC—1->4—AGLC—1->4—AGLC
>>>>> 
>>>>> Now I will rename the residues, based on their position as follow:
>>>>> 
>>>>>                           1->6 —AGM—1->4—AGF
>>>>>                         /
>>>>> AGI—1->4—AG6—1->4—AGF
>>>>> 
>>>>> Now, I am a bit confused. This time AG6 is going to be connected to AGF trough 1->4 bond, which I will add it to the residue using "O4   2C1” (which I will do similar to what I did before), but for the 1->6 connection to AGM, I would need to connect O6 of  AG6 to C1 of AGM. Should I connect it through bond O6  3C1? or O6  2C1(which would be odd!)?
>>>>> 
>>> 
>>> You can do branching with specbond.dat entries (see the manual) but GROMACS has difficulty with this.  It is trivial to perform in CHARMM.
>>> 
>>> -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 <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
> 
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