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

[Justin Lemkul]

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 nm)
Warning: Long Bond (4-11 = 0.671583 nm)
Warning: Long Bond (5-6 = 0.428864 nm)
Warning: Short Bond (5-7 = 0.044 nm)
Warning: Long Bond (7-8 = 0.648229 nm)
Warning: Long Bond (8-20 = 0.539527 nm)
Warning: Long Bond (9-21 = 0.849567 nm)
Warning: Long Bond (10-22 = 0.584145 nm)
Warning: Long Bond (11-23 = 0.637749 nm)


(b)
ERROR 4 [file topol.top, line 76]:
   No default Bond types




ERROR 7 [file topol.top, line 169]:
   No default U-B types


ERROR 19 [file topol.top, line 202]:
   No default Proper Dih. types



The missing parameters mean your atom type assignments are incorrect.


Here is mine rtp enteries.can you suggest me how to correct t?


[ UNK ]
   [ atoms ]
C1 CC3161   12.01100 1
C2 CC3161   12.01100 2
C3 CC3161   12.01100 3
C4 CC3162   12.01100 4
C5 CC3163   12.01100 5
O6 OC3C61   -0.400   6
C7 CC3161   12.01100 7
O8 OC311-0.650   8
O9 OC311-0.650   9
   O10 OC311-0.650   10
   O11 OC311-0.650   11
   O12 OC311-0.650   12
   H13 HCA1 1.00800  13
   H14 HCA1 1.00800  14
   H15 HCA1 1.00800  15
   H16 HCA1 1.00800  16
   H17 HCA1 1.00800  17
   H18 HCA1 1.00800  18
   H19 HCA1 1.00800  19
   H20 HX   0.09020
   H21 HX   0.09021
   H22 HX   0.09022
   H23 HX   0.09023
   H24 HX   0.09024



You have a mix of charges and masses in the column that should only be charges, 
so this is a fundamentally broken entry.




   [ bonds ]
C1H13
C1O12
C1C5
C1C2
C2H14
C2O9
C2C3
C3H15
C3O10
C3C4
C4H16
C4O11
C4O6
C5O6
C5C7
C5H17
C7H18
C7H19
C7O8
O8H20
O9H21
O10   H22
O11   H23
O12   H24

PDB file:-



Have you visualized these coordinates?  The format is totally broken so this is 
what pdb2gmx is complaining about.  The structure is complete nonsense.


-Justin


HEADERPROTEIN 06-JUL-17   NONE
TITLE NULL
COMPNDMOLECULE: ads1.mol
SOURCENULL
KEYWDSNULL
EXPDTANULL
AUTHORMarvin
ATOM  1  C1   UNK 0   2.462  -3.244   0.792  1.00  0.00   C
ATOM  2  C2   UNK 0   2.766  -4.727   0.446  1.00  0.00   C
ATOM  3  C3   UNK 0   1.464  -5.574   0.403  1.00  0.00   C
ATOM  4  C4   UNK 0   0.378  -4.893  -0.473  1.00  0.00   C
ATOM  5  C5   UNK 0   1.343  -2.682  -0.137  1.00  0.00   C
ATOM  6  O6   UNK 0   0.167  -3.523  -0.076  1.00  0.00   O
ATOM  7  C7   UNK 0   0.903  -1.252   0.257  1.00  0.00   C
ATOM  8  O8   UNK 0  -0.118  -0.796  -0.628  1.00  0.00   O
ATOM  9  O9   UNK 0   3.663  -5.266   1.418  1.00  0.00   O
ATOM 10  O10  UNK 0   1.748  -6.880  -0.095  1.00  0.00   O
ATOM 11  O11  UNK 0   0.692  -4.976  -1.864  1.00  0.00   O
ATOM 12  O12  UNK 0   3.652  -2.465   0.678  1.00  0.00   O
HETATM   13  H13  UNK 0   2.111  -3.189   1.801  1.00  0.00   H
HETATM   14  H14  UNK 0   3.215  -4.763  -0.524  1.00  0.00   H
HETATM   15  H15  UNK 0   1.084  -5.651   1.400  1.00  0.00   H
HETATM   16  H16  UNK 0  -0.535  -5.428  -0.314  1.00  0.00   H
HETATM   17  H17  UNK 0   1.761  -2.663  -1.122  1.00  0.00   H
HETATM   18  H18  UNK 0   1.744  -0.593   0.198  1.00  0.00   H
HETATM   19  H19  UNK 0   0.522  -1.264   1.257  1.00  0.00   H
HETATM   20  H20  UNK 0   0.223  -0.784  -1.536  1.00  0.00   H
HETATM   21  H21  UNK 0   3.249  -5.230   2.295  1.00  0.00   H
HETATM   22  H22  UNK 0   2.093  -6.813  -0.999  1.00  0.00   H
HETATM   23  H23  UNK 0   1.518  -4.498  -2.038  1.00  0.00   H
HETATM   24  H24  UNK 0   3.980  -2.507  -0.234  1.00  0.00   H
CONECT125   12   13
CONECT2139   14
CONECT324   10   15
CONECT436   11   16
CONECT5167   17
CONECT645
CONECT758   18   19
CONECT8

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

[Mohammad Hassan Khatami]

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 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   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   CC3162OC311
>> CC3162   CC3161OC311
>> 
>>> On May 24, 2017, at 11:39 AM, Justin Lemkul >> > wrote:
>>> 
>>> 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 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
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
>  before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
> 
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
>  or send 
> a mail to gmx-users-requ...@gromacs.org 
> .

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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   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   CC3162OC311
 CC3162   CC3161OC311


On May 24, 2017, at 11:39 AM, Justin Lemkul  wrote:

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 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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Mohammad Hassan Khatami]

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   CC3162OC311
 CC3162   CC3161OC311

> On May 24, 2017, at 11:39 AM, Justin Lemkul  wrote:
> 
> 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 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

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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 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



MH


On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami  wrote:

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 

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

[Mohammad Hassan Khatami]

> 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 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!)?
> 
> 
> MH
> 
>> On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami  wrote:
>> 
>> 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  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 

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

[Mohammad Hassan Khatami]

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:  
 
 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!)?


MH
 
> On May 24, 2017, at 10:47 AM, Mohammad Hassan Khatami  wrote:
> 
> 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  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 

Re: [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  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

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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


Thanks again,
MH


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 have a better understanding of what should I do. For 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, 
I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in 
the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to 
it:


Note that your residue name must be limited to 4 characters so it can properly 
be read from the input coordinates.  AGLC14 won't work.


! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of

[ bond ]
…
O4  +C1



Correct.


Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?


You should not do this.  The .vsd file is for defining virtual sites.  The IC 
lines are for the CHARMM program's internal coordinate builder, specifying some 
optimized geometry (one that the force field in total should produce, or come 
very close).  All the bonded parameters you need are already in the force field 
because they come from the corresponding .prm files.  Do not adjust bonded 
parameter files.

-Justin



Thanks again for your help.
MH



On May 19, 2017, at 5:36 PM, Justin Lemkul > wrote:



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:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.



Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick MD 
Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? 

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

[Mohammad Hassan Khatami]

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?
Thanks again,
MH
>> 
>> 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 have a better understanding of what should I do. 
>>> For each part of my polymer,i.e. the initial, the middle and the final 
>>> part, I have to modify the AGLC molecule to represent each of these parts, 
>>> seperately.
>>> So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch 
>>> from the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. 
>>> In this case, I need to create a new version of [ AGLC ] molecule (lets 
>>> call it [ AGLC14 ]) in the merged.rtp, with the changes below from the the 
>>> top_all36_carb.rtf, applied to it:
>> 
>> Note that your residue name must be limited to 4 characters so it can 
>> properly be read from the input coordinates.  AGLC14 won't work.
>> 
>>> ! equatorial-axial 1->4 linkage
>>> PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
>>> dele atom 1HO4
>>> dele atom 2HO1
>>> dele atom 2O1
>>> ATOM 1C4  CC31610.09 !
>>> ATOM 1O4  OC301-0.36 !
>>> ATOM 2C1  CC31620.29 !
>>> BOND 1O4  2C1
>>> I have to remove the HO4, HO1 and O1 lines and modify the values for the 
>>> C4, O4 and C1 atoms. Then, I need to add the bond of
>>> 
>>> [ bond ]
>>> …
>>> O4  +C1
>>> 
>> 
>> Correct.
>> 
>>> Then, I need to apply  the bonds and angles parameters in the the 
>>> top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS 
>>> CHARMM36.
>>> !IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
>>> IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
>>> IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
>>> IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
>>> IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837
>>> 
>>> I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values 
>>> into the merged.vsd file, except for the PHI values. Where (and/or how) 
>>> should I put it?
>>> Am I on the right track?
>> 
>> You should not do this.  The .vsd file is for defining virtual sites.  The 
>> IC lines are for the CHARMM program's internal coordinate builder, 
>> specifying some optimized geometry (one that the force field in total should 
>> produce, or come very close).  All the bonded parameters you need are 
>> already in the force field because they come from the corresponding .prm 
>> files.  Do not adjust bonded parameter files.
>> 
>> -Justin
>> 
>>> 
>>> Thanks again for your help.
>>> MH
>>> 
>>> 
 On May 19, 2017, at 5:36 PM, Justin Lemkul > wrote:
 
 
 
 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:
> 
> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
> 
 
 Linkages are not specific to the sugar; most are totally generic.  A few 
 comments suggest specific usage and may be corner cases, but your patches 
 will be among 14aa, 14ab, 14ba, 14bb.
 
> 
> Then, I might need to branch them with1->6 linkage.
 
 Also totally possible.
 
> I tried Glycan Reader, but itstill crashes.
> 
 
 Uploading a correctly named PDB file should work in Glycan Reader or the 
 Quick MD Simulator, but "still crashes" is not diagnostic of anything.  
 Specific help with CHARMM-GUI should be brought to their attention, though.
 
 -Justin
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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 have a better understanding of what should I do. For 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this case, 
I need to create a new version of [ AGLC ] molecule (lets call it [ AGLC14 ]) in 
the merged.rtp, with the changes below from the the top_all36_carb.rtf, applied to 
it:


Note that your residue name must be limited to 4 characters so it can properly 
be read from the input coordinates.  AGLC14 won't work.



! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of

[ bond ]
…
O4  +C1



Correct.


Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?


You should not do this.  The .vsd file is for defining virtual sites.  The IC 
lines are for the CHARMM program's internal coordinate builder, specifying some 
optimized geometry (one that the force field in total should produce, or come 
very close).  All the bonded parameters you need are already in the force field 
because they come from the corresponding .prm files.  Do not adjust bonded 
parameter files.


-Justin



Thanks again for your help.
MH



On May 19, 2017, at 5:36 PM, Justin Lemkul  wrote:



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:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.



Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick MD 
Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.

-Justin


MH



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 far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM 
.rtf files) that tell you how each residue is manipulated in the case of a 
patch; refer to the CHARMM documentation online for specifics.  The file you'll 
need is top_all36_carb.rtf.

Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.

-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



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 implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and 

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

[Mohammad Hassan Khatami]

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 
each part of my polymer,i.e. the initial, the middle and the final part, I have 
to modify the AGLC molecule to represent each of these parts, seperately.  
So, lets say to introduce the 1->4 linkage, I need to to apply 14ba patch from 
the top_all36_carb.rtf into the merged.rtp file of GROMACS CHARMM36. In this 
case, I need to create a new version of [ AGLC ] molecule (lets call it [ 
AGLC14 ]) in the merged.rtp, with the changes below from the the 
top_all36_carb.rtf, applied to it:
! equatorial-axial 1->4 linkage
PRES 14ba   0.02 ! (i)1->4(i-1) equatorial at C1 and axial at C4
dele atom 1HO4
dele atom 2HO1
dele atom 2O1
ATOM 1C4  CC31610.09 !
ATOM 1O4  OC301-0.36 !
ATOM 2C1  CC31620.29 !
BOND 1O4  2C1
I have to remove the HO4, HO1 and O1 lines and modify the values for the C4, O4 
and C1 atoms. Then, I need to add the bond of 

[ bond ]
…
O4  +C1

Then, I need to apply  the bonds and angles parameters in the the 
top_all36_carb.rtf (below), into the merged.vsd file of the GROMACS CHARMM36.
!IJKL  R(IK)   T(IKJ)PHI   T(JKL)   R(KL)
IC   1C3  1C4  1O4  2C11.5071  110.40  -86.30  121.00   1.3902  ! psi
IC   1C4  1O4  2C1  2O51.4560  121.00 -130.97  108.63   1.4470  ! phi
IC   2O5  1O4 *2C1  2C21.4470  108.63 -122.09  110.89   1.5316
IC   2O5  1O4 *2C1  2H11.4470  108.63  121.92  111.32   1.0837

I have figured out how to implement R(IK), T(IKJ), T(JKL) and R(KL) values into 
the merged.vsd file, except for the PHI values. Where (and/or how) should I put 
it?
Am I on the right track?

Thanks again for your help.
MH


> On May 19, 2017, at 5:36 PM, Justin Lemkul  wrote:
> 
> 
> 
> 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:
>> 
>> alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.
>> 
> 
> Linkages are not specific to the sugar; most are totally generic.  A few 
> comments suggest specific usage and may be corner cases, but your patches 
> will be among 14aa, 14ab, 14ba, 14bb.
> 
>> 
>> Then, I might need to branch them with1->6 linkage.
> 
> Also totally possible.
> 
>> I tried Glycan Reader, but itstill crashes.
>> 
> 
> Uploading a correctly named PDB file should work in Glycan Reader or the 
> Quick MD Simulator, but "still crashes" is not diagnostic of anything.  
> Specific help with CHARMM-GUI should be brought to their attention, though.
> 
> -Justin
> 
>> MH
>>> 
 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 far.
>>> 
>>> What you need to do depends on linkages.  There are patches (PRES in CHARMM 
>>> .rtf files) that tell you how each residue is manipulated in the case of a 
>>> patch; refer to the CHARMM documentation online for specifics.  The file 
>>> you'll need is top_all36_carb.rtf.
>>> 
>>> Otherwise, use the force field files as a template to rename your input 
>>> structure so CHARMM-GUI can process it.  This is probably the much faster 
>>> route.
>>> 
>>> -Justin
>>> 
 I'll play with these two, and I'll be back.
 MH
> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
> 
> 
> 
> 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 implemented monomers of 
>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer 
>> to the GROMACS?
>> 
> 
> Sure, you can treat it like any polymer, but you'll have to create the 
> internal monomer residues yourself from the patches in the original 
> CHARMM force field files.
> 
> Or try CHARMM-GUI; it should handle what you need and give you all the 
> necessary GROMACS inputs.
> 
> -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
> 

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

[Justin Lemkul]

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:

alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose,1->4,alpha-D-glucose.



Linkages are not specific to the sugar; most are totally generic.  A few 
comments suggest specific usage and may be corner cases, but your patches will 
be among 14aa, 14ab, 14ba, 14bb.




Then, I might need to branch them with1->6 linkage.


Also totally possible.


I tried Glycan Reader, but itstill crashes.



Uploading a correctly named PDB file should work in Glycan Reader or the Quick 
MD Simulator, but "still crashes" is not diagnostic of anything.  Specific help 
with CHARMM-GUI should be brought to their attention, though.


-Justin


MH



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 far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM 
.rtf files) that tell you how each residue is manipulated in the case of a 
patch; refer to the CHARMM documentation online for specifics.  The file you'll 
need is top_all36_carb.rtf.

Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.

-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



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 implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and give you all the 
necessary GROMACS inputs.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.




--
==

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

jalem...@outerbanks.umaryland.edu  | 
(410) 706-7441
http://mackerell.umaryland.edu/~jalemkul 


==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
 before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 


* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
 or send a mail 
to gmx-users-requ...@gromacs.org .




--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe 

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

[Mohammad Hassan Khatami]

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.


Then, I might need to branch them with1->6 linkage.
I tried Glycan Reader, but it still crashes.

MH
> 
>> 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 far.
> 
> What you need to do depends on linkages.  There are patches (PRES in CHARMM 
> .rtf files) that tell you how each residue is manipulated in the case of a 
> patch; refer to the CHARMM documentation online for specifics.  The file 
> you'll need is top_all36_carb.rtf.
> 
> Otherwise, use the force field files as a template to rename your input 
> structure so CHARMM-GUI can process it.  This is probably the much faster 
> route.
> 
> -Justin
> 
>> I'll play with these two, and I'll be back.
>> MH
>>> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
>>> 
>>> 
>>> 
>>> 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 implemented monomers of 
 alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer 
 to the GROMACS?
 
>>> 
>>> Sure, you can treat it like any polymer, but you'll have to create the 
>>> internal monomer residues yourself from the patches in the original CHARMM 
>>> force field files.
>>> 
>>> Or try CHARMM-GUI; it should handle what you need and give you all the 
>>> necessary GROMACS inputs.
>>> 
>>> -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
>>> 
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>> 
>>> ==
>>> --
>>> Gromacs Users mailing list
>>> 
>>> * Please search the archive at 
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>> 
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>> 
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send 
>>> a mail to gmx-users-requ...@gromacs.org.
>> 
> 
> -- 
> ==
> 
> 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
> 
> jalem...@outerbanks.umaryland.edu  
> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul 
> 
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List 
>  before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists 
> 
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users 
>  or send 
> a mail to gmx-users-requ...@gromacs.org 
> .

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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 to apply 
them (any suggestions?), so it did not go far.


What you need to do depends on linkages.  There are patches (PRES in CHARMM .rtf 
files) that tell you how each residue is manipulated in the case of a patch; 
refer to the CHARMM documentation online for specifics.  The file you'll need is 
top_all36_carb.rtf.


Otherwise, use the force field files as a template to rename your input 
structure so CHARMM-GUI can process it.  This is probably the much faster route.


-Justin


I'll play with these two, and I'll be back.
MH

On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:



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 implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field 
files.

Or try CHARMM-GUI; it should handle what you need and give you all the 
necessary GROMACS inputs.

-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.




--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Mohammad Hassan Khatami]

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 far.
I'll play with these two, and I'll be back.
MH
> On May 18, 2017, at 5:08 PM, Justin Lemkul  wrote:
> 
> 
> 
> 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 implemented monomers of 
>> alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to 
>> the GROMACS?
>> 
> 
> Sure, you can treat it like any polymer, but you'll have to create the 
> internal monomer residues yourself from the patches in the original CHARMM 
> force field files.
> 
> Or try CHARMM-GUI; it should handle what you need and give you all the 
> necessary GROMACS inputs.
> 
> -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
> 
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.

-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Justin Lemkul]

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 implemented monomers of 
alpha-D-glucose as ”AGLC”. Is there a way to introduce the whole polymer to the 
GROMACS?



Sure, you can treat it like any polymer, but you'll have to create the internal 
monomer residues yourself from the patches in the original CHARMM force field files.


Or try CHARMM-GUI; it should handle what you need and give you all the necessary 
GROMACS inputs.


-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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

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

[Mohammad Hassan Khatami]

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 there a way to introduce the whole polymer to the 
GROMACS?

Best,
Mohammad
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.