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

Wed May 24 17:39:21 CEST 2017

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> 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

>>
>> MH
>>
>>> On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami <mhk302 at mun.ca> wrote:
>>>
>>> Hi Justin,
>>> Here are all the errors with the (atom indices) and the "atom names”.  Based on the order of the errors I think I am making mistakes when I am trying to modify the AGLC units to connect them through O4-2C1 (O4 to the C1 of the next residue).  I am some how sure that I am making mistakes in the connecting bond part.
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>> ERROR 1 [file topol.top, line 396]: (between 16 18 24)“C4-O4-2C1” —for 2C1, or other atoms means C1 or the other atom of the next residue.
>>> No default U-B types
>>>
>>> ERROR 2 [file topol.top, line 437]: (between 37 39 45)“C4-O4-2C1”
>>> No default U-B types
>>>
>>> ERROR 3 [file topol.top, line 549]: (between 5 16 18 24)“C5-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 4 [file topol.top, line 550]: (between 12 16 18 24)“C3-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 5 [file topol.top, line 551]: (between 17 16 18 24)“H4-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 6 [file topol.top, line 552]: (between 16 18 24 25)”C4-O4-2C1-2H1”
>>> No default Proper Dih. types
>>>
>>> ERROR 7 [file topol.top, line 553]: (between 16 18 24 28)”C4-O4-2C1-2O5”
>>> No default Proper Dih. types
>>>
>>> ERROR 8 [file topol.top, line 554]: (between 16 18 24 29)”C4-O4-2C1-2C2”
>>> No default Proper Dih. types
>>>
>>> ERROR 9 [file topol.top, line 615]: (between 26 37 39 45)“C5-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 10 [file topol.top, line 616]: (between 33 37 39 45)“C3-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 11 [file topol.top, line 617]: (between 38 37 39 45)“H4-C4-O4-2C1”
>>> No default Proper Dih. types
>>>
>>> ERROR 12 [file topol.top, line 618]: (between 37 39 45 46)”C4-O4-2C1-2H1”
>>> No default Proper Dih. types
>>>
>>> ERROR 13 [file topol.top, line 619]: (between 37 39 45 49)”C4-O4-2C1-2O5”
>>> No default Proper Dih. types
>>>
>>> ERROR 14 [file topol.top, line 620]: (between 37 39 45 50)”C4-O4-2C1-2C2”
>>> No default Proper Dih. types
>>> ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>
>>> Just as a reminder, in the first step of setting up my system, I am trying to make a trimer of AGLC—1->4—AGLC—1->4—AGLC. So I modified the AGLC and made 3 copies for the initial residue, called “AGI”, the middle one, called “AGM” and the final one, called “AGF”.
>>> I removed the unwanted atoms, modified the charges and updated the indices , as described in  the CHARMM patch file. I also removed the bond associated with the atoms that I have removed.
>>> For both initial (AGI) and middle (AGM) ones I added the bond below in the [ bonds ]  parts.
>>> O4   +C1
>>> to connect the O4 to the C1 of the next residue.
>>> For the last one (AGF) I did not add any bonds.
>>>
>>> Thanks again,
>>> MH
>>>
>>>> On May 23, 2017, at 7:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>> On 5/23/17 2:16 PM, Mohammad Hassan Khatami wrote:
>>>>> Thank Justin!
>>>>> I finished adding the new “residues” in the .rtp file. pdb2gmx runs straight forward. However, while doing energy minimizations, I get several errors like the ones below, arise:
>>>>>
>>>>> ERROR 2 [file topol.top, line 396]:
>>>>> No default U-B types
>>>>> and
>>>>> ERROR 5 [file topol.top, line 550]:
>>>>> No default Proper Dih. types
>>>>>
>>>>> As it says, they might be related to the angles and dihedral parameters. Do you have any suggestion on where (and how) to add them?
>>>>
>>>> You shouldn't need to add parameters, but without knowing what is on those lines (more specifically, the associated atom types because the atom numbers will mean nothing to me) there's nothing else I can say about it.  The entirety of the carbohydrate force field should already be ported over, so missing parameters are very odd.
>>>>
>>>> -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

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