subject:"Re\: \[gmx\-users\] Re\: still can not run md for creatine"

Re: [gmx-users] Re: still can not run md for creatine

2010-11-16 Thread Justin A. Lemkul




Esteban Gabriel Vega Hissi wrote:

Justin,

Regarding the charges you mention, what do you think about RESP charges 
for this kind of compounds (drugs) parameterization?




We have not found any single charge calculation method that correctly reproduces 
the charges on Gromos96 charge groups, so further iterative refinement and 
validation is a must.  We recommend AM1-BCC for an initial charge calculation, 
as it actually produces charges that are consistently more comparable to those 
expected in the force field.


The groups in Gromos96 are very transferable across molecules, so piecing 
together a novel molecule from building blocks works quite well.  It's only for 
those unknown groups that you'd have to derive new charges.


As soon as our paper is out, I will link it from the Parameterization and PRODRG 
pages on the wiki, since this is a very common question.


-Justin


Best wishes

Esteban

--
On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul > wrote:



Just the $0.02 that I always seem to contribute in these types of
discussions - the topology you have shown below contains some likely
problems.  The charges (and massive charge group size) can lead to
artifacts.  We've got a paper due out soon about the implications of
incorrect charges, but I would advise you that this topology should
*not* be used for production simulation.  You'd be better off
spending the time to properly parameterize the molecule rather than
run a bunch of simulations and get questionable (at best) or wrong
(at worst) results.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

Olga Ivchenko wrote:


Hey Vitaly,

Thank you for your reply. Here is the files:

*itp:*
;  ;  ;   This file was generated by PRODRG version
AA081006.0504
;   PRODRG written/copyrighted by Daan van Aalten
;   and Alexander Schuettelkopf
;  ;   Questions/comments to
d...@davapc1.bioch.dundee.ac.uk

>

;  ;   When using this software in a publication, cite:
;   A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;   PRODRG - a tool for high-throughput crystallography
;   of protein-ligand complexes.
;   Acta Crystallogr. D60, 1355--1363.
;  ;  
[ moleculetype ]

 Name nrexcl
DRG  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
1OM 1  DRG OXT 1   -0.701  15.9994  
2 C 1  DRG   C 10.402  12.0110   3  
 OM 1  DRG   O 1   -0.701  15.9994   4  
CH2 1  DRG  CA 20.185  14.0270   5 N
1  DRG   N 20.468  14.0067   6   CH3
1  DRG CAG 20.201  15.0350   7 C 1

 DRG CAH 20.377  12.0110   8NZ 1
 DRG NAE 2   -0.163  14.0067   9 H 1
 DRG HA6 20.023   1.0080  10 H 1
 DRG HAE 20.024   1.0080  11NZ 1
 DRG NAD 2   -0.163  14.0067  12 H 1
 DRG HA5 20.024   1.0080  13 H 1
 DRG HAD 20.024   1.0080  
[ bonds ]

; ai  aj  fuc0, c1, ...
  2   1   20.125  1340.00.125  1340.0 ; C
 OXT 2   3   20.125  1340.00.125  1340.0 ;  
  CO 2   4   20.153   715.00.153   715.0
; C   CA 5   4   20.147   871.00.147  
871.0 ; N   CA 5   6   20.147   871.0  
 0.147   871.0 ; N  CAG 5   7   20.134
 1050.00.134  1050.0 ; N  CAH 7   8   2  
 0.134  1050.00.134  1050.0 ;   CAH  NAE 7  11  
20.134  1050.00.134  1050.0 ;   CAH  NAD 8  
9   20.100  1870.00.100  1870.0 ;   NAE  HA6
8  10   20.100  1870.00.100  1870.0 ;   NAE  HAE

   11  12   20.100  1870.00.100  1870.0 ;   NAD
 HA511  13   20.100  1870.00.100  1870.0 ;  
NAD  HAD  
[ pairs ]

; ai  aj  fuc0, c1, ...
  1   5   1   ;   OXT  
 N 2   6   1   ;
C  CAG 2   7   1   ;
C  CAH 3   5   1
  ; ON 4   8   1

Re: [gmx-users] Re: still can not run md for creatine

2010-11-15 Thread Esteban Gabriel Vega Hissi

Justin,

Regarding the charges you mention, what do you think about RESP charges for
this kind of compounds (drugs) parameterization?

Best wishes

Esteban

--
On Mon, Nov 15, 2010 at 11:12 PM, Justin A. Lemkul  wrote:

>
> Just the $0.02 that I always seem to contribute in these types of
> discussions - the topology you have shown below contains some likely
> problems.  The charges (and massive charge group size) can lead to
> artifacts.  We've got a paper due out soon about the implications of
> incorrect charges, but I would advise you that this topology should *not* be
> used for production simulation.  You'd be better off spending the time to
> properly parameterize the molecule rather than run a bunch of simulations
> and get questionable (at best) or wrong (at worst) results.
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> -Justin
>
> Olga Ivchenko wrote:
>
>>
>> Hey Vitaly,
>>
>> Thank you for your reply. Here is the files:
>>
>> *itp:*
>> ;  ;  ;   This file was generated by PRODRG version
>> AA081006.0504
>> ;   PRODRG written/copyrighted by Daan van Aalten
>> ;   and Alexander Schuettelkopf
>> ;  ;   Questions/comments to d...@davapc1.bioch.dundee.ac.uk> d...@davapc1.bioch.dundee.ac.uk>
>>
>> ;  ;   When using this software in a publication, cite:
>> ;   A. W. Schuettelkopf and D. M. F. van Aalten (2004).
>> ;   PRODRG - a tool for high-throughput crystallography
>> ;   of protein-ligand complexes.
>> ;   Acta Crystallogr. D60, 1355--1363.
>> ;  ;
>> [ moleculetype ]
>>  Name nrexcl
>> DRG  3
>>
>> [ atoms ]
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>> 1OM 1  DRG OXT 1   -0.701  15.9994   2
>> C 1  DRG   C 10.402  12.0110   3OM 1  DRG
>> O 1   -0.701  15.9994   4   CH2 1  DRG  CA 2
>>  0.185  14.0270   5 N 1  DRG   N 20.468  14.0067
>>   6   CH3 1  DRG CAG 20.201  15.0350   7
>> C 1  DRG CAH 20.377  12.0110   8NZ 1  DRG
>>   NAE 2   -0.163  14.0067   9 H 1  DRG HA6 2
>>  0.023   1.0080  10 H 1  DRG HAE 20.024   1.0080
>>  11NZ 1  DRG NAD 2   -0.163  14.0067  12
>> H 1  DRG HA5 20.024   1.0080  13 H 1  DRG
>>   HAD 20.024   1.0080
>> [ bonds ]
>> ; ai  aj  fuc0, c1, ...
>>   2   1   20.125  1340.00.125  1340.0 ; C  OXT 2
>> 3   20.125  1340.00.125  1340.0 ; CO 2   4   2
>>  0.153   715.00.153   715.0 ; C   CA 5   4   20.147
>>   871.00.147   871.0 ; N   CA 5   6   20.147
>> 871.00.147   871.0 ; N  CAG 5   7   20.134
>>  1050.00.134  1050.0 ; N  CAH 7   8   20.134
>>  1050.00.134  1050.0 ;   CAH  NAE 7  11   20.134
>>  1050.00.134  1050.0 ;   CAH  NAD 8   9   20.100
>>  1870.00.100  1870.0 ;   NAE  HA6 8  10   20.100
>>  1870.00.100  1870.0 ;   NAE  HAE11  12   20.100
>>  1870.00.100  1870.0 ;   NAD  HA511  13   20.100
>>  1870.00.100  1870.0 ;   NAD  HAD
>> [ pairs ]
>> ; ai  aj  fuc0, c1, ...
>>   1   5   1   ;   OXTN 2
>> 6   1   ; C  CAG 2   7   1
>> ; C  CAH 3   5   1
>> ; ON 4   8   1
>> ;CA  NAE 4  11   1
>> ;CA  NAD 5   9   1
>> ; N  HA6 5  10   1
>> ; N  HAE 5  12   1   ; N
>>  HA5 5  13   1   ; N  HAD
>>   6   8   1   ;   CAG  NAE 6  11
>>   1   ;   CAG  NAD 8  12   1
>>   ;   NAE  HA5 8  13   1
>>   ;   NAE  HAD 9  11   1
>>   ;   HA6  NAD10  11   1
>>   ;   HAE  NAD
>> [ angles ]
>> ; ai  aj  ak  fuc0, c1, ...
>>   1   2   3   2126.0   770.0126.0   770.0 ;   OXTC
>>  O 1   2   4   2117.0   635.0117.0   635.0 ;   OXTC
>>   CA 3   2   4   2117.0   635.0117.0   635.0 ; O
>>  C   CA 2   4   5   2109.5   520.0109.5   520.0 ; C
>>   CAN 4   5   6   2121.0   685.0121.0   685.0 ;
>>  CAN  CAG 4   5   7   2122.0   700.0122.0   700.0 ;
>>CAN  CAH 6   5   7   2117.0   635.0117.0   635.0
>> ;   CAGN  CAH 5   7   8   2

Re: [gmx-users] Re: still can not run md for creatine

2010-11-15 Thread Justin A. Lemkul



Just the $0.02 that I always seem to contribute in these types of discussions - 
the topology you have shown below contains some likely problems.  The charges 
(and massive charge group size) can lead to artifacts.  We've got a paper due 
out soon about the implications of incorrect charges, but I would advise you 
that this topology should *not* be used for production simulation.  You'd be 
better off spending the time to properly parameterize the molecule rather than 
run a bunch of simulations and get questionable (at best) or wrong (at worst) 
results.


http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

Olga Ivchenko wrote:


Hey Vitaly,

Thank you for your reply. Here is the files:

*itp:*
;  
;  
;   This file was generated by PRODRG version AA081006.0504

;   PRODRG written/copyrighted by Daan van Aalten
;   and Alexander Schuettelkopf
;  
;   Questions/comments to d...@davapc1.bioch.dundee.ac.uk 

;  
;   When using this software in a publication, cite:

;   A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;   PRODRG - a tool for high-throughput crystallography
;   of protein-ligand complexes.
;   Acta Crystallogr. D60, 1355--1363.
;  
;  


[ moleculetype ]
 Name nrexcl
DRG  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OM 1  DRG OXT 1   -0.701  15.9994  
 2 C 1  DRG   C 10.402  12.0110  
 3OM 1  DRG   O 1   -0.701  15.9994  
 4   CH2 1  DRG  CA 20.185  14.0270  
 5 N 1  DRG   N 20.468  14.0067  
 6   CH3 1  DRG CAG 20.201  15.0350  
 7 C 1  DRG CAH 20.377  12.0110  
 8NZ 1  DRG NAE 2   -0.163  14.0067  
 9 H 1  DRG HA6 20.023   1.0080  
10 H 1  DRG HAE 20.024   1.0080  
11NZ 1  DRG NAD 2   -0.163  14.0067  
12 H 1  DRG HA5 20.024   1.0080  
13 H 1  DRG HAD 20.024   1.0080  


[ bonds ]
; ai  aj  fuc0, c1, ...
   2   1   20.125  1340.00.125  1340.0 ; C  OXT  
   2   3   20.125  1340.00.125  1340.0 ; CO  
   2   4   20.153   715.00.153   715.0 ; C   CA  
   5   4   20.147   871.00.147   871.0 ; N   CA  
   5   6   20.147   871.00.147   871.0 ; N  CAG  
   5   7   20.134  1050.00.134  1050.0 ; N  CAH  
   7   8   20.134  1050.00.134  1050.0 ;   CAH  NAE  
   7  11   20.134  1050.00.134  1050.0 ;   CAH  NAD  
   8   9   20.100  1870.00.100  1870.0 ;   NAE  HA6  
   8  10   20.100  1870.00.100  1870.0 ;   NAE  HAE  
  11  12   20.100  1870.00.100  1870.0 ;   NAD  HA5  
  11  13   20.100  1870.00.100  1870.0 ;   NAD  HAD  


[ pairs ]
; ai  aj  fuc0, c1, ...
   1   5   1   ;   OXTN  
   2   6   1   ; C  CAG  
   2   7   1   ; C  CAH  
   3   5   1   ; ON  
   4   8   1   ;CA  NAE  
   4  11   1   ;CA  NAD  
   5   9   1   ; N  HA6  
   5  10   1   ; N  HAE  
   5  12   1   ; N  HA5  
   5  13   1   ; N  HAD  
   6   8   1   ;   CAG  NAE  
   6  11   1   ;   CAG  NAD  
   8  12   1   ;   NAE  HA5  
   8  13   1   ;   NAE  HAD  
   9  11   1   ;   HA6  NAD  
  10  11   1   ;   HAE  NAD  


[ angles ]
; ai  aj  ak  fuc0, c1, ...
   1   2   3   2126.0   770.0126.0   770.0 ;   OXT
CO  
   1   2   4   2117.0   635.0117.0   635.0 ;   OXT
C   CA  
   3   2   4   2117.0   635.0117.0   635.0 ; O
C   CA  
   2   4   5   2109.5   520.0109.5   520.0 ; C   
CAN  
   4   5   6   2121.0   685.0121.0   685.0 ;CAN  
CAG  
   4   5   7   2122.0   700.0122.0   700.0 ;CAN  
CAH  
   6   5   7   2117.0   635.0117.0   635.0 ;   CAGN  
CAH  
   5   7   8   2120.0   670.0120.0   670.0 ; N  CAH  
NAE  
   5   7  11   2120.0   670.0120.0   670.0 ;

Re: [gmx-users] Re: still can not run md for creatine

2010-11-15 Thread Mark Abraham


On 16/11/2010 6:22 AM, Vitaly Chaban wrote:

Olga -

What is gromos43a1.ff? I do not remember the files with ff-extension
in gromacs. I am sure you should include the topology files in the


There's a new force field organization in 4.5.x. PRODRG still presumes 
the previous organization, which leads to the OP's first symptoms. 
However the real issue is not wanting to use the gmx force field at all.


Mark


inverse order as compared to what is below:
1) general FF with atoms, bonds, angles, etc (~ include "gromos43a1.ff");
2) molecule definition, its own atoms, bonds, etc (~ include "creatine.itp")

After that, you'll probably get another error, and it will be more informative.

Good luck!

Vitaly





On Mon, Nov 15, 2010 at 12:09 PM, Olga Ivchenko  wrote:

Hey Vitaly,

Thank you for your reply. Here is the files:

itp:
;
;
;   This file was generated by PRODRG version AA081006.0504
;   PRODRG written/copyrighted by Daan van Aalten
;   and Alexander Schuettelkopf
;
;   Questions/comments to d...@davapc1.bioch.dundee.ac.uk
;
;   When using this software in a publication, cite:
;   A. W. Schuettelkopf and D. M. F. van Aalten (2004).
;   PRODRG - a tool for high-throughput crystallography
;   of protein-ligand complexes.
;   Acta Crystallogr. D60, 1355--1363.
;
;

[ moleculetype ]
  Name nrexcl
DRG  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
  1OM 1  DRG OXT 1   -0.701  15.9994
  2 C 1  DRG   C 10.402  12.0110
  3OM 1  DRG   O 1   -0.701  15.9994
  4   CH2 1  DRG  CA 20.185  14.0270
  5 N 1  DRG   N 20.468  14.0067
  6   CH3 1  DRG CAG 20.201  15.0350
  7 C 1  DRG CAH 20.377  12.0110
  8NZ 1  DRG NAE 2   -0.163  14.0067
  9 H 1  DRG HA6 20.023   1.0080
 10 H 1  DRG HAE 20.024   1.0080
 11NZ 1  DRG NAD 2   -0.163  14.0067
 12 H 1  DRG HA5 20.024   1.0080
 13 H 1  DRG HAD 20.024   1.0080

[ bonds ]
; ai  aj  fuc0, c1, ...
2   1   20.125  1340.00.125  1340.0 ; C  OXT
2   3   20.125  1340.00.125  1340.0 ; CO
2   4   20.153   715.00.153   715.0 ; C   CA
5   4   20.147   871.00.147   871.0 ; N   CA
5   6   20.147   871.00.147   871.0 ; N  CAG
5   7   20.134  1050.00.134  1050.0 ; N  CAH
7   8   20.134  1050.00.134  1050.0 ;   CAH  NAE
7  11   20.134  1050.00.134  1050.0 ;   CAH  NAD
8   9   20.100  1870.00.100  1870.0 ;   NAE  HA6
8  10   20.100  1870.00.100  1870.0 ;   NAE  HAE
   11  12   20.100  1870.00.100  1870.0 ;   NAD  HA5
   11  13   20.100  1870.00.100  1870.0 ;   NAD  HAD

[ pairs ]
; ai  aj  fuc0, c1, ...
1   5   1   ;   OXTN
2   6   1   ; C  CAG
2   7   1   ; C  CAH
3   5   1   ; ON
4   8   1   ;CA  NAE
4  11   1   ;CA  NAD
5   9   1   ; N  HA6
5  10   1   ; N  HAE
5  12   1   ; N  HA5
5  13   1   ; N  HAD
6   8   1   ;   CAG  NAE
6  11   1   ;   CAG  NAD
8  12   1   ;   NAE  HA5
8  13   1   ;   NAE  HAD
9  11   1   ;   HA6  NAD
   10  11   1   ;   HAE  NAD

[ angles ]
; ai  aj  ak  fuc0, c1, ...
1   2   3   2126.0   770.0126.0   770.0 ;   OXTC
O
1   2   4   2117.0   635.0117.0   635.0 ;   OXTC
CA
3   2   4   2117.0   635.0117.0   635.0 ; OC
CA
2   4   5   2109.5   520.0109.5   520.0 ; C   CA
N
4   5   6   2121.0   685.0121.0   685.0 ;CAN
CAG
4   5   7   2122.0   700.0122.0   700.0 ;CAN
CAH
6   5   7   2117.0   635.0117.0   635.0 ;   CAGN
CAH
5   7   8   2120.0   670.0120.0   670.0 ; N  CAH
NAE
5   7  11   2120.0   670.0120.0   670.0 ; N  CAH
NAD
8   7  11   2120.0

Re: [gmx-users] Re: still can not run md for creatine

Re: [gmx-users] Re: still can not run md for creatine

Re: [gmx-users] Re: still can not run md for creatine

Re: [gmx-users] Re: still can not run md for creatine

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