Re: [gmx-users] No default Ryckaert-Bell. types

[Baolin Huang]

Hi Dan and all guys,
Thanks for your answers. I find that the OPLS-AA force field does not contain 
the dihedral force-field parameters of the Chain_C. Actually, my Chain_C was a 
hydroxyapatite (HAP, inorganic material) model. I also notice that the bond 
types of HAP in the ffbonded.itp file are missing.
Following are some parameters from my ffbonded.itp file.
[ dihedraltypes ]
;  ijkl   func coefficients
C3 CT NT C3  3  1.78866   3.49154   0.53555  -5.81576   
0.0   0.0 ; (From wildcard) amine all-atom
[ bondtypes ]
; ij  func   b0  kb
  OWHW  10.09572   502080.0   ; For TIP4F Water - wlj 1/98
 
My question is that what are the meanings of the i, j, k, l, func, 
coefficients, b0, and kb? How to find the values of those of HAP? Just list 
some [bonds] and [dihedrals] of my Chain_C as follows.
[ bonds ]
 O1  P27
 O10 P27
 O13 P27
 O14 P27
 O2  P28
[ dihedrals ] 
O1P27   O10  O13
O1P27   O10  O14
O1P27   O13  O10
O1P27   O13  O14
O1P27   O14  O13
 
Thanks for your time and any suggestions.
Kind regards,
Baolin
 
 
 
 
 
-- Original --
From:  "Dan Gil";
Date:  Tue, Aug 14, 2018 04:39 AM
To:  "gmx-users"; 

Subject:  Re: [gmx-users] No default Ryckaert-Bell. types

 
Hello,

This is telling you that the OPLS-AA force field does not have the dihedral
force-field parameters for your molecule (topol_Other_chain_C.itp) of the
Ryckaert-Bell type. Your exact problem might be:
(1) There is something wrong with the molecule topology.
(2) OPLS-AA really doesn't have the dihedral force-field parameters, and
you need to use another force-field.

If your molecule is a simple hydrocarbon, it is unlikely that OPLS-AA has
missing parameters.

Dan

On Sat, Aug 11, 2018 at 10:52 AM, Baolin Huang  wrote:

> Dear All,
>   I experienced an error as follows: (I used the OPLS-AA force field)
>   ERROR 48600 [file topol_Other_chain_C.itp, line 144934]:
>   No default Ryckaert-Bell. types
>
>
> Anyone can help?
> Kind regards,
>
>
> --
>
> Dr. Baolin Huang
> Lecturer, School of Life Sciences, Guangzhou University
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
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> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] No default Ryckaert-Bell. types

[Dan Gil]

Hello,

This is telling you that the OPLS-AA force field does not have the dihedral
force-field parameters for your molecule (topol_Other_chain_C.itp) of the
Ryckaert-Bell type. Your exact problem might be:
(1) There is something wrong with the molecule topology.
(2) OPLS-AA really doesn't have the dihedral force-field parameters, and
you need to use another force-field.

If your molecule is a simple hydrocarbon, it is unlikely that OPLS-AA has
missing parameters.

Dan

On Sat, Aug 11, 2018 at 10:52 AM, Baolin Huang  wrote:

> Dear All,
>   I experienced an error as follows: (I used the OPLS-AA force field)
>   ERROR 48600 [file topol_Other_chain_C.itp, line 144934]:
>   No default Ryckaert-Bell. types
>
>
> Anyone can help?
> Kind regards,
>
>
> --
>
> Dr. Baolin Huang
> Lecturer, School of Life Sciences, Guangzhou University
> --
> 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.
>
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[gmx-users] No default Ryckaert-Bell. types

[Baolin Huang]

Dear All,
  I experienced an error as follows: (I used the OPLS-AA force field)
  ERROR 48600 [file topol_Other_chain_C.itp, line 144934]:
  No default Ryckaert-Bell. types


Anyone can help?
Kind regards,


--
 
Dr. Baolin Huang
Lecturer, School of Life Sciences, Guangzhou University
-- 
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Re: [gmx-users] No default Ryckaert-Bell. types

[Justin Lemkul]

On 9/3/15 7:19 AM, Daniele Veclani wrote:

Dear Naga Rajesh Tummala

I read in the manual the part relating to Ryckaert-Bell. angles.

But I did not understand how to enter the 5 parameters.

Do you tell me where I can find a guide?



You enter the parameters with a text editor.  The mechanics are simple, but 
deriving those values requires knowledge of the force field parametrization 
methodology.  For that, you have to go into the literature, do some QM, then do 
parameter fitting.


-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

==
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Re: [gmx-users] No default Ryckaert-Bell. types

[Daniele Veclani]

Dear Naga Rajesh Tummala

I read in the manual the part relating to Ryckaert-Bell. angles.

But I did not understand how to enter the 5 parameters.

Do you tell me where I can find a guide?

Best regard

2015-09-02 18:02 GMT+02:00 Naga Rajesh Tummala :

> In the dihedrals section, similar to the bonds and angles section, the
> parameters are followed after the dihedral type..
>
> 2 1 3 4 3 v0 v1 v2 v3 v4 v5  for RB type
>
>
>
> On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani  >
> wrote:
>
> > Thank you for your answer.
> >
> > how can I put these parameters in the .top file?
> >
> > Best regard.
> >
> >
> >
> > 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala :
> >
> > > The parameters for the RB dihedral in line 227 are not described in the
> > > opls forcefield. Either you can provide the parameters in your top file
> > or
> > > include the dihedral paramters in the opls forcefield files tht comes
> > with
> > > gromacs.
> > >
> > >
> > >
> > > On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani <
> > danielevecl...@gmail.com
> > > >
> > > wrote:
> > >
> > > > Dear users.
> > > >
> > > >
> > > > I'm trying to build the file .top for a molecule with opls FF.
> > > >
> > > > To do this I used MKTOP but when I run grompp I get this error:
> > > >
> > > > "ERROR 23 [file nor.top, line 227]:
> > > >  No default Ryckaert-Bell. types"
> > > >
> > > > This is my file .top:
> > > >
> > > > [ moleculetype ]
> > > > ; Namenrexcl
> > > > MOL 3
> > > >
> > > > [ atoms ]
> > > > ;   nr   type  resnr residue  atom   cgnr charge   mass
> > > > typeBchargeB  massB
> > > > 1  opls_268   1   MOL  O11   -0.61100 15.9994
> > > > 2  opls_270   1   MOL  H11   0.44100 1.008
> > > > 3  opls_267   1   MOL  C11   0.81100 12.011
> > > > 4  opls_269   1   MOL  O21   -0.54900 15.9994
> > > > 5  opls_141   1   MOL  C22   -0.52100 12.011
> > > > 6  opls_145   1   MOL  C33   0.07300 12.011
> > > > 7  opls_140   1   MOL  H23   0.14200 1.008
> > > > 8  opls_280   1   MOL  C44   0.62500 12.011
> > > > 9  opls_281   1   MOL  O34   -578.0 15.9994
> > > >10  opls_145   1   MOL  C55   -0.12600 12.011
> > > >11  opls_145B   1   MOL  C66   0.13300 12.011
> > > >12  opls_145   1   MOL  C77   -0.26700 12.011
> > > >13  opls_146   1   MOL  H37   0.19900 1.008
> > > >14  opls_718   1   MOL  C88   0.27000 12.011
> > > >15  opls_719   1   MOL  F18   -0.18000 18.9984
> > > >16  opls_145   1   MOL  C99   0.03900 12.011
> > > >17  opls_145   1   MOL  C1010   -0.24200 12.011
> > > >18  opls_146   1   MOL  H410   0.15800 1.008
> > > >19  opls_902   1   MOL  N19   -0.11600 14.0067
> > > >20  opls_908   1   MOL  C1111   -0.12000 12.011
> > > >21  opls_140   1   MOL  H511   0.09300 1.008
> > > >22  opls_140   1   MOL  H611   0.07400 1.008
> > > >23  opls_907   1   MOL  C1212   0.11300 12.011
> > > >24  opls_140   1   MOL  H712   0.07600 1.008
> > > >25  opls_140   1   MOL  H812   0.05500 1.008
> > > >26  opls_908   1   MOL  C1313   -0.12400 12.011
> > > >27  opls_140   1   MOL  H913   0.07300 1.008
> > > >28  opls_140   1   MOL  H1013   0.07700 1.008
> > > >29  opls_907   1   MOL  C1414   0.10200 12.011
> > > >30  opls_140   1   MOL  H1114   0.08500 1.008
> > > >31  opls_140   1   MOL  H1214   0.05300 1.008
> > > >32  opls_901   1   MOL  N212   -0.71000 14.0067
> > > >33  opls_910   1   MOL  H1312   0.35700 1.008
> > > >34  opls_902   1   MOL  N33   -0.11200 14.0067
> > > >35  opls_908   1   MOL  C1515   0.19100 12.011
> > > >36  opls_140   1   MOL  H1415   0.03700 1.008
> > > >37  opls_140   1   MOL  H1515   0.0 1.008
> > > >38  opls_135   1   MOL  C1616   -0.26000 12.011
> > > >39  opls_140   1   MOL  H1616   0.08900 1.008
> > > >40  opls_140   1   MOL  H1716   0.08000 1.008
> > > >41  opls_140   1   MOL  H1816   0.07500 1.008
> > > >
> > > >
> > > >
> > > >
> > > > [ bonds ]
> > > > 1 2 1   0.099  462750.4
> > > > 1 3 1   0.133  376560.0
> > > > 3 4 1   0.121  476976.0
> > > > 3 5 1   0.150  343088.0
> > > > 5 6 1   0.137  357313.6
> > > > 5 8 1   0.145  343088.0
> > > > 6 7 1   0.108  284512.0
> > > > 6 34 1   0.135  402500.8
> > > 

[gmx-users] No default Ryckaert-Bell. types

[Daniele Veclani]

Dear users.


I'm trying to build the file .top for a molecule with opls FF.

To do this I used MKTOP but when I run grompp I get this error:

"ERROR 23 [file nor.top, line 227]:
 No default Ryckaert-Bell. types"

This is my file .top:

[ moleculetype ]
; Namenrexcl
MOL 3

[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass
typeBchargeB  massB
1  opls_268   1   MOL  O11   -0.61100 15.9994
2  opls_270   1   MOL  H11   0.44100 1.008
3  opls_267   1   MOL  C11   0.81100 12.011
4  opls_269   1   MOL  O21   -0.54900 15.9994
5  opls_141   1   MOL  C22   -0.52100 12.011
6  opls_145   1   MOL  C33   0.07300 12.011
7  opls_140   1   MOL  H23   0.14200 1.008
8  opls_280   1   MOL  C44   0.62500 12.011
9  opls_281   1   MOL  O34   -578.0 15.9994
   10  opls_145   1   MOL  C55   -0.12600 12.011
   11  opls_145B   1   MOL  C66   0.13300 12.011
   12  opls_145   1   MOL  C77   -0.26700 12.011
   13  opls_146   1   MOL  H37   0.19900 1.008
   14  opls_718   1   MOL  C88   0.27000 12.011
   15  opls_719   1   MOL  F18   -0.18000 18.9984
   16  opls_145   1   MOL  C99   0.03900 12.011
   17  opls_145   1   MOL  C1010   -0.24200 12.011
   18  opls_146   1   MOL  H410   0.15800 1.008
   19  opls_902   1   MOL  N19   -0.11600 14.0067
   20  opls_908   1   MOL  C1111   -0.12000 12.011
   21  opls_140   1   MOL  H511   0.09300 1.008
   22  opls_140   1   MOL  H611   0.07400 1.008
   23  opls_907   1   MOL  C1212   0.11300 12.011
   24  opls_140   1   MOL  H712   0.07600 1.008
   25  opls_140   1   MOL  H812   0.05500 1.008
   26  opls_908   1   MOL  C1313   -0.12400 12.011
   27  opls_140   1   MOL  H913   0.07300 1.008
   28  opls_140   1   MOL  H1013   0.07700 1.008
   29  opls_907   1   MOL  C1414   0.10200 12.011
   30  opls_140   1   MOL  H1114   0.08500 1.008
   31  opls_140   1   MOL  H1214   0.05300 1.008
   32  opls_901   1   MOL  N212   -0.71000 14.0067
   33  opls_910   1   MOL  H1312   0.35700 1.008
   34  opls_902   1   MOL  N33   -0.11200 14.0067
   35  opls_908   1   MOL  C1515   0.19100 12.011
   36  opls_140   1   MOL  H1415   0.03700 1.008
   37  opls_140   1   MOL  H1515   0.0 1.008
   38  opls_135   1   MOL  C1616   -0.26000 12.011
   39  opls_140   1   MOL  H1616   0.08900 1.008
   40  opls_140   1   MOL  H1716   0.08000 1.008
   41  opls_140   1   MOL  H1816   0.07500 1.008




[ bonds ]
1 2 1   0.099  462750.4
1 3 1   0.133  376560.0
3 4 1   0.121  476976.0
3 5 1   0.150  343088.0
5 6 1   0.137  357313.6
5 8 1   0.145  343088.0
6 7 1   0.108  284512.0
6 34 1   0.135  402500.8
8 9 1   0.125  476976.0
8 10 1   0.147  334720.0
10 11 1   0.141  392459.2
10 12 1   0.141  392459.2
11 17 1   0.141  392459.2
11 34 1   0.140  20.0
12 13 1   0.108  307105.6
12 14 1   0.136  392459.2
14 15 1   0.135  351456.0
14 16 1   0.142  392459.2
16 17 1   0.140  392459.2
16 19 1   0.140  402500.8
17 18 1   0.108  307105.6
19 20 1   0.148  319657.6
19 26 1   0.146  319657.6
20 21 1   0.109  284512.0
20 22 1   0.110  284512.0
20 23 1   0.153  224262.4
23 24 1   0.109  284512.0
23 25 1   0.109  284512.0
23 32 1   0.146  319657.6
26 27 1   0.109  284512.0
26 28 1   0.111  284512.0
26 29 1   0.154  224262.4
29 30 1   0.110  284512.0
29 31 1   0.109  284512.0
29 32 1   0.146  319657.6
32 33 1   0.102  363171.2
34 35 1   0.147  319657.6
35 36 1   0.109  284512.0
35 37 1   0.109  284512.0
35 38 1   0.153  224262.4
38 39 1   0.109  284512.0
38 40 1   0.109  284512.0
38 41 1   0.109  284512.0


[ angles ]
1 3 4 1  122.613  669.440
1 3 5 1  115.207  585.760
2 1 3 1  108.493  292.880
3 5 6 1  117.303  585.760
3 5 8 1  122.815  585.760
4 3 5 1  122.180  669.440
5 6 7 1  118.516  418.400
5 6 34 1  124.720  669.440
5 8 9 1  123.231  669.440
5 8 10 1  115.012  585.760
6 5 8 1  119.879  585.760
6 34 11 1  119.618  669.440
6 34 35 1  118.344  418.400
7 6 34 1  116.763  669.440
8 10 11 1  121.987  585.760
8 10 12 1  119.361  711.280
9 8 10 1  121.756  669.440
10 11 17 1  119.731  527.184
10 11 34 1  118.777  669.440
10 12 13 1  118.733  292.880
10 12 14 1  120.570  527.184
11 10 12 1  118.650  527.184
11 17 16 1  121.908  527.184
11 17 18 1  119.847  292.880
11 34 35 1  121.996  669.440
12 14 15 1  118.664  669.440
12 14 16 1  122.613  527.184
13 12 14 1  120.674  292.880
14 16 17 1  116.514  

Re: [gmx-users] No default Ryckaert-Bell. types

[Daniele Veclani]

Thank you for your answer.

how can I put these parameters in the .top file?

Best regard.



2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala :

> The parameters for the RB dihedral in line 227 are not described in the
> opls forcefield. Either you can provide the parameters in your top file or
> include the dihedral paramters in the opls forcefield files tht comes with
> gromacs.
>
>
>
> On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani  >
> wrote:
>
> > Dear users.
> >
> >
> > I'm trying to build the file .top for a molecule with opls FF.
> >
> > To do this I used MKTOP but when I run grompp I get this error:
> >
> > "ERROR 23 [file nor.top, line 227]:
> >  No default Ryckaert-Bell. types"
> >
> > This is my file .top:
> >
> > [ moleculetype ]
> > ; Namenrexcl
> > MOL 3
> >
> > [ atoms ]
> > ;   nr   type  resnr residue  atom   cgnr charge   mass
> > typeBchargeB  massB
> > 1  opls_268   1   MOL  O11   -0.61100 15.9994
> > 2  opls_270   1   MOL  H11   0.44100 1.008
> > 3  opls_267   1   MOL  C11   0.81100 12.011
> > 4  opls_269   1   MOL  O21   -0.54900 15.9994
> > 5  opls_141   1   MOL  C22   -0.52100 12.011
> > 6  opls_145   1   MOL  C33   0.07300 12.011
> > 7  opls_140   1   MOL  H23   0.14200 1.008
> > 8  opls_280   1   MOL  C44   0.62500 12.011
> > 9  opls_281   1   MOL  O34   -578.0 15.9994
> >10  opls_145   1   MOL  C55   -0.12600 12.011
> >11  opls_145B   1   MOL  C66   0.13300 12.011
> >12  opls_145   1   MOL  C77   -0.26700 12.011
> >13  opls_146   1   MOL  H37   0.19900 1.008
> >14  opls_718   1   MOL  C88   0.27000 12.011
> >15  opls_719   1   MOL  F18   -0.18000 18.9984
> >16  opls_145   1   MOL  C99   0.03900 12.011
> >17  opls_145   1   MOL  C1010   -0.24200 12.011
> >18  opls_146   1   MOL  H410   0.15800 1.008
> >19  opls_902   1   MOL  N19   -0.11600 14.0067
> >20  opls_908   1   MOL  C1111   -0.12000 12.011
> >21  opls_140   1   MOL  H511   0.09300 1.008
> >22  opls_140   1   MOL  H611   0.07400 1.008
> >23  opls_907   1   MOL  C1212   0.11300 12.011
> >24  opls_140   1   MOL  H712   0.07600 1.008
> >25  opls_140   1   MOL  H812   0.05500 1.008
> >26  opls_908   1   MOL  C1313   -0.12400 12.011
> >27  opls_140   1   MOL  H913   0.07300 1.008
> >28  opls_140   1   MOL  H1013   0.07700 1.008
> >29  opls_907   1   MOL  C1414   0.10200 12.011
> >30  opls_140   1   MOL  H1114   0.08500 1.008
> >31  opls_140   1   MOL  H1214   0.05300 1.008
> >32  opls_901   1   MOL  N212   -0.71000 14.0067
> >33  opls_910   1   MOL  H1312   0.35700 1.008
> >34  opls_902   1   MOL  N33   -0.11200 14.0067
> >35  opls_908   1   MOL  C1515   0.19100 12.011
> >36  opls_140   1   MOL  H1415   0.03700 1.008
> >37  opls_140   1   MOL  H1515   0.0 1.008
> >38  opls_135   1   MOL  C1616   -0.26000 12.011
> >39  opls_140   1   MOL  H1616   0.08900 1.008
> >40  opls_140   1   MOL  H1716   0.08000 1.008
> >41  opls_140   1   MOL  H1816   0.07500 1.008
> >
> >
> >
> >
> > [ bonds ]
> > 1 2 1   0.099  462750.4
> > 1 3 1   0.133  376560.0
> > 3 4 1   0.121  476976.0
> > 3 5 1   0.150  343088.0
> > 5 6 1   0.137  357313.6
> > 5 8 1   0.145  343088.0
> > 6 7 1   0.108  284512.0
> > 6 34 1   0.135  402500.8
> > 8 9 1   0.125  476976.0
> > 8 10 1   0.147  334720.0
> > 10 11 1   0.141  392459.2
> > 10 12 1   0.141  392459.2
> > 11 17 1   0.141  392459.2
> > 11 34 1   0.140  20.0
> > 12 13 1   0.108  307105.6
> > 12 14 1   0.136  392459.2
> > 14 15 1   0.135  351456.0
> > 14 16 1   0.142  392459.2
> > 16 17 1   0.140  392459.2
> > 16 19 1   0.140  402500.8
> > 17 18 1   0.108  307105.6
> > 19 20 1   0.148  319657.6
> > 19 26 1   0.146  319657.6
> > 20 21 1   0.109  284512.0
> > 20 22 1   0.110  284512.0
> > 20 23 1   0.153  224262.4
> > 23 24 1   0.109  284512.0
> > 23 25 1   0.109  284512.0
> > 23 32 1   0.146  319657.6
> > 26 27 1   0.109  284512.0
> > 26 28 1   0.111  284512.0
> > 26 29 1   0.154  224262.4
> > 29 30 1   0.110  284512.0
> > 29 31 1   0.109  284512.0
> > 29 32 1   0.146  319657.6
> > 32 33 1   0.102  363171.2
> > 34 35 1   0.147  319657.6
> > 35 36 1   0.109  284512.0
> > 35 37 1   0.109  284512.0
> > 35 

Re: [gmx-users] No default Ryckaert-Bell. types

[Naga Rajesh Tummala]

The parameters for the RB dihedral in line 227 are not described in the
opls forcefield. Either you can provide the parameters in your top file or
include the dihedral paramters in the opls forcefield files tht comes with
gromacs.



On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani 
wrote:

> Dear users.
>
>
> I'm trying to build the file .top for a molecule with opls FF.
>
> To do this I used MKTOP but when I run grompp I get this error:
>
> "ERROR 23 [file nor.top, line 227]:
>  No default Ryckaert-Bell. types"
>
> This is my file .top:
>
> [ moleculetype ]
> ; Namenrexcl
> MOL 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
> 1  opls_268   1   MOL  O11   -0.61100 15.9994
> 2  opls_270   1   MOL  H11   0.44100 1.008
> 3  opls_267   1   MOL  C11   0.81100 12.011
> 4  opls_269   1   MOL  O21   -0.54900 15.9994
> 5  opls_141   1   MOL  C22   -0.52100 12.011
> 6  opls_145   1   MOL  C33   0.07300 12.011
> 7  opls_140   1   MOL  H23   0.14200 1.008
> 8  opls_280   1   MOL  C44   0.62500 12.011
> 9  opls_281   1   MOL  O34   -578.0 15.9994
>10  opls_145   1   MOL  C55   -0.12600 12.011
>11  opls_145B   1   MOL  C66   0.13300 12.011
>12  opls_145   1   MOL  C77   -0.26700 12.011
>13  opls_146   1   MOL  H37   0.19900 1.008
>14  opls_718   1   MOL  C88   0.27000 12.011
>15  opls_719   1   MOL  F18   -0.18000 18.9984
>16  opls_145   1   MOL  C99   0.03900 12.011
>17  opls_145   1   MOL  C1010   -0.24200 12.011
>18  opls_146   1   MOL  H410   0.15800 1.008
>19  opls_902   1   MOL  N19   -0.11600 14.0067
>20  opls_908   1   MOL  C1111   -0.12000 12.011
>21  opls_140   1   MOL  H511   0.09300 1.008
>22  opls_140   1   MOL  H611   0.07400 1.008
>23  opls_907   1   MOL  C1212   0.11300 12.011
>24  opls_140   1   MOL  H712   0.07600 1.008
>25  opls_140   1   MOL  H812   0.05500 1.008
>26  opls_908   1   MOL  C1313   -0.12400 12.011
>27  opls_140   1   MOL  H913   0.07300 1.008
>28  opls_140   1   MOL  H1013   0.07700 1.008
>29  opls_907   1   MOL  C1414   0.10200 12.011
>30  opls_140   1   MOL  H1114   0.08500 1.008
>31  opls_140   1   MOL  H1214   0.05300 1.008
>32  opls_901   1   MOL  N212   -0.71000 14.0067
>33  opls_910   1   MOL  H1312   0.35700 1.008
>34  opls_902   1   MOL  N33   -0.11200 14.0067
>35  opls_908   1   MOL  C1515   0.19100 12.011
>36  opls_140   1   MOL  H1415   0.03700 1.008
>37  opls_140   1   MOL  H1515   0.0 1.008
>38  opls_135   1   MOL  C1616   -0.26000 12.011
>39  opls_140   1   MOL  H1616   0.08900 1.008
>40  opls_140   1   MOL  H1716   0.08000 1.008
>41  opls_140   1   MOL  H1816   0.07500 1.008
>
>
>
>
> [ bonds ]
> 1 2 1   0.099  462750.4
> 1 3 1   0.133  376560.0
> 3 4 1   0.121  476976.0
> 3 5 1   0.150  343088.0
> 5 6 1   0.137  357313.6
> 5 8 1   0.145  343088.0
> 6 7 1   0.108  284512.0
> 6 34 1   0.135  402500.8
> 8 9 1   0.125  476976.0
> 8 10 1   0.147  334720.0
> 10 11 1   0.141  392459.2
> 10 12 1   0.141  392459.2
> 11 17 1   0.141  392459.2
> 11 34 1   0.140  20.0
> 12 13 1   0.108  307105.6
> 12 14 1   0.136  392459.2
> 14 15 1   0.135  351456.0
> 14 16 1   0.142  392459.2
> 16 17 1   0.140  392459.2
> 16 19 1   0.140  402500.8
> 17 18 1   0.108  307105.6
> 19 20 1   0.148  319657.6
> 19 26 1   0.146  319657.6
> 20 21 1   0.109  284512.0
> 20 22 1   0.110  284512.0
> 20 23 1   0.153  224262.4
> 23 24 1   0.109  284512.0
> 23 25 1   0.109  284512.0
> 23 32 1   0.146  319657.6
> 26 27 1   0.109  284512.0
> 26 28 1   0.111  284512.0
> 26 29 1   0.154  224262.4
> 29 30 1   0.110  284512.0
> 29 31 1   0.109  284512.0
> 29 32 1   0.146  319657.6
> 32 33 1   0.102  363171.2
> 34 35 1   0.147  319657.6
> 35 36 1   0.109  284512.0
> 35 37 1   0.109  284512.0
> 35 38 1   0.153  224262.4
> 38 39 1   0.109  284512.0
> 38 40 1   0.109  284512.0
> 38 41 1   0.109  284512.0
>
>
> [ angles ]
> 1 3 4 1  122.613  669.440
> 1 3 5 1  115.207  585.760
> 2 1 3 1  108.493  292.880
> 3 5 6 1  117.303  585.760
> 3 5 8 1  122.815  585.760
> 4 3 5 1  122.180  669.440
> 5 6 7 1  118.516  418.400
> 5 6 34 1  124.720  669.440
> 5 8 9 1  123.231  669.440
> 5 8 10 1  

Re: [gmx-users] No default Ryckaert-Bell. types

[Naga Rajesh Tummala]

In the dihedrals section, similar to the bonds and angles section, the
parameters are followed after the dihedral type..

2 1 3 4 3 v0 v1 v2 v3 v4 v5  for RB type



On Wed, Sep 2, 2015 at 11:48 AM, Daniele Veclani 
wrote:

> Thank you for your answer.
>
> how can I put these parameters in the .top file?
>
> Best regard.
>
>
>
> 2015-09-02 17:34 GMT+02:00 Naga Rajesh Tummala :
>
> > The parameters for the RB dihedral in line 227 are not described in the
> > opls forcefield. Either you can provide the parameters in your top file
> or
> > include the dihedral paramters in the opls forcefield files tht comes
> with
> > gromacs.
> >
> >
> >
> > On Wed, Sep 2, 2015 at 11:28 AM, Daniele Veclani <
> danielevecl...@gmail.com
> > >
> > wrote:
> >
> > > Dear users.
> > >
> > >
> > > I'm trying to build the file .top for a molecule with opls FF.
> > >
> > > To do this I used MKTOP but when I run grompp I get this error:
> > >
> > > "ERROR 23 [file nor.top, line 227]:
> > >  No default Ryckaert-Bell. types"
> > >
> > > This is my file .top:
> > >
> > > [ moleculetype ]
> > > ; Namenrexcl
> > > MOL 3
> > >
> > > [ atoms ]
> > > ;   nr   type  resnr residue  atom   cgnr charge   mass
> > > typeBchargeB  massB
> > > 1  opls_268   1   MOL  O11   -0.61100 15.9994
> > > 2  opls_270   1   MOL  H11   0.44100 1.008
> > > 3  opls_267   1   MOL  C11   0.81100 12.011
> > > 4  opls_269   1   MOL  O21   -0.54900 15.9994
> > > 5  opls_141   1   MOL  C22   -0.52100 12.011
> > > 6  opls_145   1   MOL  C33   0.07300 12.011
> > > 7  opls_140   1   MOL  H23   0.14200 1.008
> > > 8  opls_280   1   MOL  C44   0.62500 12.011
> > > 9  opls_281   1   MOL  O34   -578.0 15.9994
> > >10  opls_145   1   MOL  C55   -0.12600 12.011
> > >11  opls_145B   1   MOL  C66   0.13300 12.011
> > >12  opls_145   1   MOL  C77   -0.26700 12.011
> > >13  opls_146   1   MOL  H37   0.19900 1.008
> > >14  opls_718   1   MOL  C88   0.27000 12.011
> > >15  opls_719   1   MOL  F18   -0.18000 18.9984
> > >16  opls_145   1   MOL  C99   0.03900 12.011
> > >17  opls_145   1   MOL  C1010   -0.24200 12.011
> > >18  opls_146   1   MOL  H410   0.15800 1.008
> > >19  opls_902   1   MOL  N19   -0.11600 14.0067
> > >20  opls_908   1   MOL  C1111   -0.12000 12.011
> > >21  opls_140   1   MOL  H511   0.09300 1.008
> > >22  opls_140   1   MOL  H611   0.07400 1.008
> > >23  opls_907   1   MOL  C1212   0.11300 12.011
> > >24  opls_140   1   MOL  H712   0.07600 1.008
> > >25  opls_140   1   MOL  H812   0.05500 1.008
> > >26  opls_908   1   MOL  C1313   -0.12400 12.011
> > >27  opls_140   1   MOL  H913   0.07300 1.008
> > >28  opls_140   1   MOL  H1013   0.07700 1.008
> > >29  opls_907   1   MOL  C1414   0.10200 12.011
> > >30  opls_140   1   MOL  H1114   0.08500 1.008
> > >31  opls_140   1   MOL  H1214   0.05300 1.008
> > >32  opls_901   1   MOL  N212   -0.71000 14.0067
> > >33  opls_910   1   MOL  H1312   0.35700 1.008
> > >34  opls_902   1   MOL  N33   -0.11200 14.0067
> > >35  opls_908   1   MOL  C1515   0.19100 12.011
> > >36  opls_140   1   MOL  H1415   0.03700 1.008
> > >37  opls_140   1   MOL  H1515   0.0 1.008
> > >38  opls_135   1   MOL  C1616   -0.26000 12.011
> > >39  opls_140   1   MOL  H1616   0.08900 1.008
> > >40  opls_140   1   MOL  H1716   0.08000 1.008
> > >41  opls_140   1   MOL  H1816   0.07500 1.008
> > >
> > >
> > >
> > >
> > > [ bonds ]
> > > 1 2 1   0.099  462750.4
> > > 1 3 1   0.133  376560.0
> > > 3 4 1   0.121  476976.0
> > > 3 5 1   0.150  343088.0
> > > 5 6 1   0.137  357313.6
> > > 5 8 1   0.145  343088.0
> > > 6 7 1   0.108  284512.0
> > > 6 34 1   0.135  402500.8
> > > 8 9 1   0.125  476976.0
> > > 8 10 1   0.147  334720.0
> > > 10 11 1   0.141  392459.2
> > > 10 12 1   0.141  392459.2
> > > 11 17 1   0.141  392459.2
> > > 11 34 1   0.140  20.0
> > > 12 13 1   0.108  307105.6
> > > 12 14 1   0.136  392459.2
> > > 14 15 1   0.135  351456.0
> > > 14 16 1   0.142  392459.2
> > > 16 17 1   0.140  392459.2
> > > 16 19 1   0.140  402500.8
> > > 17 18 1   0.108  307105.6
> > > 19 20 1   0.148  319657.6
> > > 19 26 1   0.146  319657.6
> > > 20 21 1   

Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/3/15 12:00 AM, Kevin C Chan wrote:

Thanks Justin,

I have long been confused by atom names and types in Gromacs topology. I
have just went through the manual again, and it confirms me that what we
read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are
atomtypes. In other words, what you have listed in the last email

   C  CT_2   N  CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C  CT_2   NT CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C_3CT_2   N  CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro COO- terminus.
   C_3CT_2   NT CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro COO- terminus.

which was extracted from ffbonded.itp is composed of atomtypes. Meanwhile
what I have stated in the brackets - (CD N CA C), (CD N CA CB) or (CD N CA
HA) are by myself read from the topology file after pdb2gmx. To be exact, I
read

[ dihedrals ]
;  aiajakal functc0c1c2
c3c4c5
12 1 4 5 3
12 1 4 6 3
12 1 415 3

​​
​from the topology and refer the numbers (e.g. 12 1 4 15) to the above
directive ​[ atoms ] to find out that it is (CD N CA C). We can also read
from directive ​[ atoms ] that under the type column, it should be
(opls_296 opls_309 opls_285 opls_271). So which is the atomtypes, (CD N CA
C) or (opls_296 opls_309 opls_285 opls_271)? It seems (opls_296 opls_309
opls_285 opls_271) are the atomtypes, but why the itp states  (C CT_2 N
CT_3)?

And how can I refer my topology to this line of parameter when it deals (CD
N CA C) or (opls_296 opls_309 opls_285 opls_271)?



Refer to ffnonbonded.itp.  The first column (ignore the fact that it says name 
as it is actually a type) is the opls_* atom type for nonbonded interactions, 
the second column is the translated bonded type.  There are fewer bonded types 
(less diversity in interactions) and this convention removes the need for tons 
of redundant parameters.


-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

==
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[gmx-users] No default Ryckaert-Bell. types for proline

[Kevin C Chan]

Thanks Justin,

I'm sorry that I'm not clear with what do you mean by so you can likely
just use the same parameters in ffbonded.itp for this dihedral in the
zwitterionic form.

Also as I have mentioned before, when I look into the line 161, it refers
to a dihedral term concerning (CD N CA C) which is not able to be found in
ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N
CA HA) which are also not found in itp do not report such error and I was
successful to grompp after commenting out the line 161. So why would this
happen?


Thanks in advance,
Kevin

On 2 Jun, 2015, at 20:05, Justin Lemkul jalem...@vt.edu
javascript:_e(%7B%7D,'cvml','jalem...@vt.edu'); wrote:



On 6/1/15 12:25 PM, Kevin C Chan wrote:

pdb2gmx command:

gmx_d pdb2gmx -f proline.pdb -ter  15: (OPLS-AA/L all-atom force field

(2001 aminoacid dihedrals))  1: TIP4P  TIP 4-point, recommended  1:

PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one

residue)  1: PRO-ZWITTERION_COO- (only use with zwitterions containing

exactly one residue)


(I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing

exactly one residue) but the result was the same)


Screen-out:

http://pastebin.com/CuMa7aZ7#


topology:

http://pastebin.com/FSbcFGYR




It appears that there are simply no parameters in the OPLS-AA force field
for this entity.  Whether or not this is because OPLS-AA doesn't officially
have parameters for it or they are just missing from the GROMACS
implementation is something you'd have to dig into, but largely it seems
that all dihedral parameters for the N- and C-terminal forms of PRO are all
the same, so you can likely just use the same parameters in ffbonded.itp
for this dihedral in the zwitterionic form.

-Justin

Thanks in advance,

Kevin


On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul jalem...@vt.edu
javascript:_e(%7B%7D,'cvml','jalem...@vt.edu'); wrote:




On 6/1/15 12:09 PM, Kevin C Chan wrote:


​Thanks Justin,


I did not but I tried just now. The aforementioned dihedral terms ​remain

along with the errors.



Please provide your full pdb2gmx command, all screen output, and full

topology.  Use file sharing services, pastebin, etc. as needed.


-Justin



 Thanks in advance,

Kevin


On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu
javascript:_e(%7B%7D,'cvml','jalem...@vt.edu'); wrote:




On 6/1/15 10:57 AM, Kevin C Chan wrote:


 Dear Users,


I am testing with OPLSSaa force-field of proline. First I arbitrarily

extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro

and

top are however not suitable for further grompp (even minimization). The

error messages are as follows:


ERROR 1 [file topol.top, line 161]:

No default Ryckaert-Bell. types


When I look into the line 161, it refers to a dihedral term concerning

(CD

N CA C) which is not able to be found in ffbonded.itp. However, other

dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not

found in itp do not report such error and I was successful to grompp

after

commenting out the line 161.


Why would this happen?



 Did you choose the proper PRO-ZWITTERION-* termini when running

pdb2gmx?


-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
javascript:_e(%7B%7D,'cvml','jalem...@outerbanks.umaryland.edu'); | (410)
706-7441

http://mackerell.umaryland.edu/~jalemkul


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--

==


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
javascript:_e(%7B%7D,'cvml','jalem...@outerbanks.umaryland.edu'); | (410)
706-7441

http://mackerell.umaryland.edu/~jalemkul


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Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Kevin C Chan]

Thanks Justin,

I have long been confused by atom names and types in Gromacs topology. I
have just went through the manual again, and it confirms me that what we
read directly in ffbonded.itp under GMXHOME/share/gromacs/top/oplsaa.ff are
atomtypes. In other words, what you have listed in the last email

  C  CT_2   N  CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
  C  CT_2   NT CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
  C_3CT_2   N  CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro COO- terminus.
  C_3CT_2   NT CT_33 -5.72371 -18.33847  -5.23419  29.29636
0.0   0.0 ; Pro COO- terminus.

which was extracted from ffbonded.itp is composed of atomtypes. Meanwhile
what I have stated in the brackets - (CD N CA C), (CD N CA CB) or (CD N CA
HA) are by myself read from the topology file after pdb2gmx. To be exact, I
read

[ dihedrals ]
;  aiajakal functc0c1c2
   c3c4c5
   12 1 4 5 3
   12 1 4 6 3
   12 1 415 3

​​
​from the topology and refer the numbers (e.g. 12 1 4 15) to the above
directive ​[ atoms ] to find out that it is (CD N CA C). We can also read
from directive ​[ atoms ] that under the type column, it should be
(opls_296 opls_309 opls_285 opls_271). So which is the atomtypes, (CD N CA
C) or (opls_296 opls_309 opls_285 opls_271)? It seems (opls_296 opls_309
opls_285 opls_271) are the atomtypes, but why the itp states  (C CT_2 N
CT_3)?

And how can I refer my topology to this line of parameter when it deals (CD
N CA C) or (opls_296 opls_309 opls_285 opls_271)?

Regards,
Kevin
​​


On Wed, Jun 3, 2015 at 10:11 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/2/15 8:51 PM, Kevin C Chan wrote:

 Thanks Justin,

 I'm sorry that I'm not clear with what do you mean by so you can likely
 just use the same parameters in ffbonded.itp for this dihedral in the
 zwitterionic form.


 The Pro dihedral term for this torsion is the same, irrespective of
 whether it's N- or C-terminal.  From ffbonded.itp:

   C  CT_2   N  CT_33 -5.72371 -18.33847  -5.23419
 29.29636 0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C  CT_2   NT CT_33 -5.72371 -18.33847  -5.23419
 29.29636 0.0   0.0 ; Pro (fit to AM1) CD-N-CA-C, JT-R 2/10/97
   C_3CT_2   N  CT_33 -5.72371 -18.33847  -5.23419
 29.29636 0.0   0.0 ; Pro COO- terminus.
   C_3CT_2   NT CT_33 -5.72371 -18.33847  -5.23419
 29.29636 0.0   0.0 ; Pro COO- terminus.

 All the same, so the parameters for the zwitterionic species can likely be
 copied to your missing interaction.

  Also as I have mentioned before, when I look into the line 161, it refers
 to a dihedral term concerning (CD N CA C) which is not able to be found in
 ffbonded.itp. However, other dihedral terms such as (CD N CA CB) or (CD N
 CA HA) which are also not found in itp do not report such error and I was


 Atom names and atom types are entirely different concepts.  grompp doesn't
 care what you call your atoms (atom name), but it does care what chemical
 characteristics they have (atom type).

  successful to grompp after commenting out the line 161. So why would this
 happen?


 Don't ever comment out lines because of issues like this.  By doing so,
 you're saying that torsion contributes nothing to the energy function,
 which is wrong.  I suggest copying the above parameters to the correct
 sequence of atom types.  Stuff like this happens all the time.  Force
 fields are massive entities, and are added to incrementally as need
 arises.  A zwitterionic proline is probably not something that people
 commonly use, and its the most complex case due to the chemical nature of
 it.  It's entirely possible that the .tdb entries were simply added by
 analogy to existing groups as a convenience and never fully tested.


 -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

 ==
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Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/1/15 12:25 PM, Kevin C Chan wrote:

pdb2gmx command:
gmx_d pdb2gmx -f proline.pdb -ter  15: (OPLS-AA/L all-atom force field
(2001 aminoacid dihedrals))  1: TIP4P  TIP 4-point, recommended  1:
PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one
residue)  1: PRO-ZWITTERION_COO- (only use with zwitterions containing
exactly one residue)

(I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing
exactly one residue) but the result was the same)

Screen-out:
http://pastebin.com/CuMa7aZ7#

topology:
http://pastebin.com/FSbcFGYR




It appears that there are simply no parameters in the OPLS-AA force field for 
this entity.  Whether or not this is because OPLS-AA doesn't officially have 
parameters for it or they are just missing from the GROMACS implementation is 
something you'd have to dig into, but largely it seems that all dihedral 
parameters for the N- and C-terminal forms of PRO are all the same, so you can 
likely just use the same parameters in ffbonded.itp for this dihedral in the 
zwitterionic form.


-Justin


Thanks in advance,
Kevin

On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul jalem...@vt.edu wrote:




On 6/1/15 12:09 PM, Kevin C Chan wrote:


​Thanks Justin,

I did not but I tried just now. The aforementioned dihedral terms ​remain
along with the errors.



Please provide your full pdb2gmx command, all screen output, and full
topology.  Use file sharing services, pastebin, etc. as needed.

-Justin


  Thanks in advance,

Kevin

On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote:




On 6/1/15 10:57 AM, Kevin C Chan wrote:

  Dear Users,


I am testing with OPLSSaa force-field of proline. First I arbitrarily
extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro
and
top are however not suitable for further grompp (even minimization). The
error messages are as follows:

ERROR 1 [file topol.top, line 161]:
 No default Ryckaert-Bell. types

When I look into the line 161, it refers to a dihedral term concerning
(CD
N CA C) which is not able to be found in ffbonded.itp. However, other
dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
found in itp do not report such error and I was successful to grompp
after
commenting out the line 161.

Why would this happen?


  Did you choose the proper PRO-ZWITTERION-* termini when running

pdb2gmx?

-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

==
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--
==

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

==
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--
==

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

==
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Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Kevin C Chan]

​Thanks Justin,

I did not but I tried just now. The aforementioned dihedral terms ​remain
along with the errors.

Thanks in advance,
Kevin

On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/1/15 10:57 AM, Kevin C Chan wrote:

 Dear Users,

 I am testing with OPLSSaa force-field of proline. First I arbitrarily
 extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and
 top are however not suitable for further grompp (even minimization). The
 error messages are as follows:

 ERROR 1 [file topol.top, line 161]:
No default Ryckaert-Bell. types

 When I look into the line 161, it refers to a dihedral term concerning (CD
 N CA C) which is not able to be found in ffbonded.itp. However, other
 dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
 found in itp do not report such error and I was successful to grompp after
 commenting out the line 161.

 Why would this happen?


 Did you choose the proper PRO-ZWITTERION-* termini when running pdb2gmx?

 -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!

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Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Kevin C Chan]

pdb2gmx command:
gmx_d pdb2gmx -f proline.pdb -ter  15: (OPLS-AA/L all-atom force field
(2001 aminoacid dihedrals))  1: TIP4P  TIP 4-point, recommended  1:
PRO-ZWITTERION_NH2+ (only use with zwitterions containing exactly one
residue)  1: PRO-ZWITTERION_COO- (only use with zwitterions containing
exactly one residue)

(I have also tried 4: ZWITTERION_NH3+ (only use with zwitterions containing
exactly one residue) but the result was the same)

Screen-out:
http://pastebin.com/CuMa7aZ7#

topology:
http://pastebin.com/FSbcFGYR


Thanks in advance,
Kevin

On Tue, Jun 2, 2015 at 12:11 AM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/1/15 12:09 PM, Kevin C Chan wrote:

 ​Thanks Justin,

 I did not but I tried just now. The aforementioned dihedral terms ​remain
 along with the errors.


 Please provide your full pdb2gmx command, all screen output, and full
 topology.  Use file sharing services, pastebin, etc. as needed.

 -Justin


  Thanks in advance,
 Kevin

 On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote:



 On 6/1/15 10:57 AM, Kevin C Chan wrote:

  Dear Users,

 I am testing with OPLSSaa force-field of proline. First I arbitrarily
 extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro
 and
 top are however not suitable for further grompp (even minimization). The
 error messages are as follows:

 ERROR 1 [file topol.top, line 161]:
 No default Ryckaert-Bell. types

 When I look into the line 161, it refers to a dihedral term concerning
 (CD
 N CA C) which is not able to be found in ffbonded.itp. However, other
 dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
 found in itp do not report such error and I was successful to grompp
 after
 commenting out the line 161.

 Why would this happen?


  Did you choose the proper PRO-ZWITTERION-* termini when running
 pdb2gmx?

 -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!

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 * 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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/1/15 10:57 AM, Kevin C Chan wrote:

Dear Users,

I am testing with OPLSSaa force-field of proline. First I arbitrarily
extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and
top are however not suitable for further grompp (even minimization). The
error messages are as follows:

ERROR 1 [file topol.top, line 161]:
   No default Ryckaert-Bell. types

When I look into the line 161, it refers to a dihedral term concerning (CD
N CA C) which is not able to be found in ffbonded.itp. However, other
dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
found in itp do not report such error and I was successful to grompp after
commenting out the line 161.

Why would this happen?



Did you choose the proper PRO-ZWITTERION-* termini when running pdb2gmx?

-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 
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Re: [gmx-users] No default Ryckaert-Bell. types for proline

[Justin Lemkul]

On 6/1/15 12:09 PM, Kevin C Chan wrote:

​Thanks Justin,

I did not but I tried just now. The aforementioned dihedral terms ​remain
along with the errors.



Please provide your full pdb2gmx command, all screen output, and full topology. 
 Use file sharing services, pastebin, etc. as needed.


-Justin


Thanks in advance,
Kevin

On Mon, Jun 1, 2015 at 11:13 PM, Justin Lemkul jalem...@vt.edu wrote:




On 6/1/15 10:57 AM, Kevin C Chan wrote:


Dear Users,

I am testing with OPLSSaa force-field of proline. First I arbitrarily
extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and
top are however not suitable for further grompp (even minimization). The
error messages are as follows:

ERROR 1 [file topol.top, line 161]:
No default Ryckaert-Bell. types

When I look into the line 161, it refers to a dihedral term concerning (CD
N CA C) which is not able to be found in ffbonded.itp. However, other
dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
found in itp do not report such error and I was successful to grompp after
commenting out the line 161.

Why would this happen?



Did you choose the proper PRO-ZWITTERION-* termini when running pdb2gmx?

-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

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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

==
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[gmx-users] No default Ryckaert-Bell. types for proline

[Kevin C Chan]

Dear Users,

I am testing with OPLSSaa force-field of proline. First I arbitrarily
extract a single PRO from a pdb and fed into pdb2gmx. The resulted gro and
top are however not suitable for further grompp (even minimization). The
error messages are as follows:

ERROR 1 [file topol.top, line 161]:
  No default Ryckaert-Bell. types

When I look into the line 161, it refers to a dihedral term concerning (CD
N CA C) which is not able to be found in ffbonded.itp. However, other
dihedral terms such as (CD N CA CB) or (CD N CA HA) which are also not
found in itp do not report such error and I was successful to grompp after
commenting out the line 161.

Why would this happen?


Thanks in advance,
Kevin
City University of Hong Kong
-- 
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