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

Mohammad Hassan Khatami mhk302 at mun.ca
Wed May 24 18:04:57 CEST 2017

Sorry for that. Here are the types.
atom       type
C1       CC3162
O4       OC311
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> 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>> 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

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