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

On 7/11/17 2:46 AM, Akash Ranjan wrote: Sir, I am facing difficulty in making topology for a simple molecule using CHARMM36 but i am facing certain difficulty in that such as (a)Warning: Long Bond (3-10 = 0.566378 nm) Warning: Long Bond (3-4 = 0.426475 nm) Warning: Long Bond (4-16 = 0.59

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

Thanks Justin! It worked. All bonds are now in place. I’ll play with the branching a bit and will make a new ticket, if I had a problem. Thank again, MH > On May 24, 2017, at 1:04 PM, Justin Lemkul wrote: > > > > On 5/24/17 12:04 PM, Mohammad Hassan Khatami wrote: >> Sorry

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

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 top_all36_carb.rtf). -Justin C4 CC3161 C5 CC3163 C3 CC3161 H4

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

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,

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

On 5/24/17 11:35 AM, Mohammad Hassan Khatami wrote: On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami 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

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

> On May 24, 2017, at 11:31 AM, Mohammad Hassan Khatami 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! > Now I

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

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. 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:

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

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

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

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

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

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]:

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

On 5/22/17 1:09 AM, Mohammad Hassan Khatami wrote: Hi Justin, I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.) Thank you! I think I now

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

Hi Justin, I am asked to focus on learning how to change and update the CHARMM36 parameters, so I could implement the future changes and patches easier. (Thus, I am not focused in the Glycan Reader, at the moment.) Thank you! I think I now have a better understanding of what should I do. For

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

On 5/19/17 9:57 AM, Mohammad Hassan Khatami wrote: First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below:

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

First, I am looking for 1->4 and 1->6 linkages. In the top_all36_carb.rtf file I found different linkages for beta-glucose, but non for alpha-glucose. I am trying to make a simple chain with 1->4 linkages like below: alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.

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

On 5/18/17 6:35 PM, Mohammad Hassan Khatami wrote: Thanks Justin. I have tried the CHARMM-GUI but it crashed. I might need to modify the order of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual on how

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

Thanks Justin. I have tried the CHARMM-GUI but it crashed. I might need to modify the order of the atoms in my PDB file, which I have created using GLYCAM-Web GUI. I have downloaded the “toppar_c36_feb16” but I did not find a manual on how to apply them (any suggestions?), so it did not go

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

On 5/18/17 4:57 PM, Mohammad Hassan Khatami wrote: Hi, I am trying to run simulations on alpha-D-glucose polymers. I have done these simulations using AMBER and I am wondering if it is possible to run them employing CHARMM36 in GROMACS, as well? It seams that CHARMM36 in GROMACS has only

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

Hi, I am trying to run simulations on alpha-D-glucose polymers. I have done these simulations using AMBER and I am wondering if it is possible to run them employing CHARMM36 in GROMACS, as well? It seams that CHARMM36 in GROMACS has only implemented monomers of alpha-D-glucose as ”AGLC”. Is