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

[Mohammad Hassan Khatami]

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