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

Justin Lemkul jalemkul at vt.edu
Wed May 24 19:04:25 CEST 2017

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 


> 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


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


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