[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.
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.
>>> Now I will rename the residues, based on their position as follow:
>>> 1->6 —AGM—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.
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