Re: [gmx-users] if PRODRG calculate incorrectly

[Mark Abraham]

On 23/09/2011 4:48 PM, ahmet y?ld?r?m wrote:

Dear users,

If I obtain/generate the topology file for a ligand using another 
program (except PRODRG);


1) How can I arrange .itp file? Because it seems very complicate.


Yes, this is not an easy thing to do. Modelling an arbitrary organic 
compound is a difficult task. There are links from the link I provided 
last time that will help you.


2) Justin 
tutorial:http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
We will make use of two files that PRODRG gives us. Save the output of 
the field "The GROMOS87/GROMACS coordinate file (polar/aromatic 
hydrogens)" into a text file called "jz4.gro" and "The GROMACS 
topology" into a file called "drg.itp."

Then how can I generate .gro file using another program?


Again, follow the links, please.

Mark



I was obtaining .gro and .itp files using PRODRG but PRODRG is giving 
improper results/output.


best regards


2011/9/17 Mark Abraham >


On 17/09/2011 11:28 PM, ahmet y?ld?r?m wrote:

Dear Tsjerk and Justin,

Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand
coordinates/topologies?


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

Mark

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Ahmet YILDIRIM




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Re: [gmx-users] if PRODRG calculate incorrectly

[ahmet yıldırım]

Dear users,

If I obtain/generate the topology file for a ligand using another program
(except PRODRG);

1) How can I arrange .itp file? Because it seems very complicate.
2) Justin tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html
We will make use of two files that PRODRG gives us. Save the output of the
field "The GROMOS87/GROMACS coordinate file (polar/aromatic hydrogens)" into
a text file called "jz4.gro" and "The GROMACS topology" into a file called
"drg.itp."
Then how can I generate .gro file using another program?

I was obtaining .gro and .itp files using PRODRG but PRODRG is giving
improper results/output.

best regards


2011/9/17 Mark Abraham 

> On 17/09/2011 11:28 PM, ahmet yıldırım wrote:
>
>> Dear Tsjerk and Justin,
>>
>> Thanks for your reply. I will contact the PRODRG developers.
>> can you suggest anyway/anytool for generating ligand
>> coordinates/topologies?
>>
>
> http://www.gromacs.org/**Documentation/How-tos/Steps_**
> to_Perform_a_Simulation
>
> Mark
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Searchbefore
>  posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read 
> http://www.gromacs.org/**Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
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Re: [gmx-users] if PRODRG calculate incorrectly

[Mark Abraham]

On 17/09/2011 11:28 PM, ahmet yıldırım wrote:

Dear Tsjerk and Justin,

Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand 
coordinates/topologies?


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

Mark
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Re: [gmx-users] if PRODRG calculate incorrectly

[ahmet yıldırım]

Dear Tsjerk and Justin,

Thanks for your reply. I will contact the PRODRG developers.
can you suggest anyway/anytool for generating ligand coordinates/topologies?


Thanks in advance

17 Eylül 2011 15:58 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>> I have a problem related to PRODRG.
>>
>> Chirality:NO
>> Full charges: YES
>> Energy minimization: NO
>>
>> _*İnput file name:TRS.pdb*_
>> HETATM 1803  C   TRS B 232  38.588  -4.733  65.956  1.00 17.99
>>   C ANISOU 1803  C   TRS B 232 2126   1948   2760   -378 45-81
>> C HETATM 1804  C1  TRS B 232  40.103  -5.057  65.899  1.00 16.81
>>   C ANISOU 1804  C1  TRS B 232 1642   1577   3168   -531171
>>  120   C HETATM 1805  C2  TRS B 232  37.795  -5.994  66.343  1.00
>> 20.76   C ANISOU 1805  C2  TRS B 232 2790   2021   3077 67
>>  141   -408   C HETATM 1806  C3  TRS B 232  38.160  -3.717  67.031
>>  1.00 16.86   C ANISOU 1806  C3  TRS B 232 2240   1557   2611
>> -491  8   -192   C HETATM 1807  N   TRS B 232  38.227  -4.154
>>  64.652  1.00 18.26   N ANISOU 1807  N   TRS B 232 2336   2520
>> 2083   -166 46   -112   N HETATM 1808  O1  TRS B 232  40.741
>>  -4.020  65.158  1.00 17.53   O ANISOU 1808  O1  TRS B 232 1921
>>   1579   3163   -225147197   O HETATM 1809  O2  TRS B 232
>>  37.871  -6.803  65.211  1.00 23.91   O ANISOU 1809  O2  TRS B 232
>>   3018   2456   3610-48-86   -450   O HETATM 1810  O3  TRS B 232
>>  38.871  -2.531  66.874  1.00 18.28   O ANISOU 1810  O3  TRS B
>> 232 2677   1594   2673197 -4-52   O
>>
>> I get the output _as the following file1.itp_ from your PRODRG server for
>> TRS ligand before 3-4 months. I think this calculate is correct:
>> *_file1.itp_*
>> 
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS  3
>>
>> [ atoms ]
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>> 1OA 1  TRS  O1 1   -0.240  15.9994   2
>>  H  1  TRS HAA 10.052   1.0080   3   CH2 1  TRS
>>  C1 10.061  14.0270   4   CH1 1  TRS   C 1
>>  0.127  12.0110   5   CH2 1  TRS  C3 20.090  14.0270
>>   6OA 1  TRS  O3 2   -0.165  15.9994   7
>>  H  1  TRS HAC 20.075   1.0080   8NL 1  TRS
>>   N 30.876  14.0067   9 H 1  TRS HAE 3
>>  0.041   1.0080  10 H 1  TRS HAF 30.042   1.0080
>>  11 H 1  TRS HAD 30.041   1.0080  12
>> CH2 1  TRS  C2 40.090  14.0270  13OA 1  TRS
>>  O2 4   -0.165  15.9994  14H  1  TRS HAB 4
>>  0.075   1.0080  
>>
>>
>> But Now, That is, today,  I get the output _as the following file2.itp_
>> from your PRODRG server for TRS ligand.
>> *_file2.itp_*
>> .
>> [ moleculetype ]
>> ; Name nrexcl
>> TRS  3
>>
>> [ atoms ]
>> ;   nr  type  resnr resid  atom  cgnr   charge mass
>> 1OA 1  TRS  O1 1   -0.173  15.9994   2
>> H 1  TRS H13 10.061   1.0080   3   CH2 1  TRS
>>C1 10.165  14.0270   4  CCL4 1  TRS   C 1
>>  0.177  12.0110   5   CH2 1  TRS  C3 10.165  14.0270
>>   6OA 1  TRS  O3 1   -0.174  15.9994   7
>> H 1  TRS H33 10.062   1.0080   8NL 1  TRS
>> N 10.675  14.0067   9 H 1  TRS  H2 1
>>  0.014   1.0080  10 H 1  TRS  H3 10.014   1.0080
>>  11 H 1  TRS  H1 10.014   1.0080  12
>> CH2 1  TRS  C2 20.144  14.0270  13OA 1  TRS
>>  O2 2   -0.198  15.9994  14 H 1  TRS H23 2
>>  0.054   1.0080  
>>
>> Now, I think PRODRG calculate incorrectly  cgnr   charge
>>
>>
> I agree with Tsjerk that you should contact the PRODRG developers regarding
> the differences, but I would also say that neither of these files is
> correct. PRODRG has never given reliable charges.  See, for instance
> (something I posted dozens of times before):
>
> http://pubs.acs.org/doi/abs/**10.1021/ci100335w
>
> -Justin
>
>
>  What should I do? can you help me?
>>
>> --
>> Ahmet YILDIRIM
>>
>>
> --
> ==**==
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
> gmx-users mai

Re: [gmx-users] if PRODRG calculate incorrectly

[Justin A. Lemkul]

ahmet yıldırım wrote:

Dear users,
I have a problem related to PRODRG.

Chirality:NO
Full charges: YES
Energy minimization: NO

_*İnput file name:TRS.pdb*_
HETATM 1803  C   TRS B 232  38.588  -4.733  65.956  1.00 
17.99   C 
ANISOU 1803  C   TRS B 232 2126   1948   2760   -378 45
-81   C 
HETATM 1804  C1  TRS B 232  40.103  -5.057  65.899  1.00 
16.81   C 
ANISOU 1804  C1  TRS B 232 1642   1577   3168   -531171
120   C 
HETATM 1805  C2  TRS B 232  37.795  -5.994  66.343  1.00 
20.76   C 
ANISOU 1805  C2  TRS B 232 2790   2021   3077 67141   
-408   C 
HETATM 1806  C3  TRS B 232  38.160  -3.717  67.031  1.00 
16.86   C 
ANISOU 1806  C3  TRS B 232 2240   1557   2611   -491  8   
-192   C 
HETATM 1807  N   TRS B 232  38.227  -4.154  64.652  1.00 
18.26   N 
ANISOU 1807  N   TRS B 232 2336   2520   2083   -166 46   
-112   N 
HETATM 1808  O1  TRS B 232  40.741  -4.020  65.158  1.00 
17.53   O 
ANISOU 1808  O1  TRS B 232 1921   1579   3163   -225147
197   O 
HETATM 1809  O2  TRS B 232  37.871  -6.803  65.211  1.00 
23.91   O 
ANISOU 1809  O2  TRS B 232 3018   2456   3610-48-86   
-450   O 
HETATM 1810  O3  TRS B 232  38.871  -2.531  66.874  1.00 
18.28   O 
ANISOU 1810  O3  TRS B 232 2677   1594   2673197 -4
-52   O


I get the output _as the following file1.itp_ from your PRODRG server 
for TRS ligand before 3-4 months. I think this calculate is correct:

*_file1.itp_*

[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.240  15.9994  
 2H  1  TRS HAA 10.052   1.0080  
 3   CH2 1  TRS  C1 10.061  14.0270  
 4   CH1 1  TRS   C 10.127  12.0110  
 5   CH2 1  TRS  C3 20.090  14.0270  
 6OA 1  TRS  O3 2   -0.165  15.9994  
 7H  1  TRS HAC 20.075   1.0080  
 8NL 1  TRS   N 30.876  14.0067  
 9 H 1  TRS HAE 30.041   1.0080  
10 H 1  TRS HAF 30.042   1.0080  
11 H 1  TRS HAD 30.041   1.0080  
12   CH2 1  TRS  C2 40.090  14.0270  
13OA 1  TRS  O2 4   -0.165  15.9994  
14H  1  TRS HAB 40.075   1.0080  




But Now, That is, today,  I get the output _as the following file2.itp_ 
from your PRODRG server for TRS ligand.

*_file2.itp_*
.
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.173  15.9994  
 2 H 1  TRS H13 10.061   1.0080  
 3   CH2 1  TRS  C1 10.165  14.0270  
 4  CCL4 1  TRS   C 10.177  12.0110  
 5   CH2 1  TRS  C3 10.165  14.0270  
 6OA 1  TRS  O3 1   -0.174  15.9994  
 7 H 1  TRS H33 10.062   1.0080  
 8NL 1  TRS   N 10.675  14.0067  
 9 H 1  TRS  H2 10.014   1.0080  
10 H 1  TRS  H3 10.014   1.0080  
11 H 1  TRS  H1 10.014   1.0080  
12   CH2 1  TRS  C2 20.144  14.0270  
13OA 1  TRS  O2 2   -0.198  15.9994  
14 H 1  TRS H23 20.054   1.0080  



Now, I think PRODRG calculate incorrectly  cgnr   charge



I agree with Tsjerk that you should contact the PRODRG developers regarding the 
differences, but I would also say that neither of these files is correct. 
PRODRG has never given reliable charges.  See, for instance (something I posted 
dozens of times before):


http://pubs.acs.org/doi/abs/10.1021/ci100335w

-Justin


What should I do? can you help me?

--
Ahmet YILDIRIM



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] if PRODRG calculate incorrectly

[Tsjerk Wassenaar]

Hi Ahmet,

The PRODRG server is not related to Gromacs. If you encounter problems
pertaining to the server or the outcome from it, you should drop a
line to the PRODRG development team.

Cheers,

Tsjerk

2011/9/17 ahmet yıldırım :
> Dear users,
> I have a problem related to PRODRG.
>
> Chirality:NO
> Full charges: YES
> Energy minimization: NO
>
> İnput file name:TRS.pdb
> HETATM 1803  C   TRS B 232  38.588  -4.733  65.956  1.00 17.99
> C
> ANISOU 1803  C   TRS B 232 2126   1948   2760   -378 45    -81
> C
> HETATM 1804  C1  TRS B 232  40.103  -5.057  65.899  1.00 16.81
> C
> ANISOU 1804  C1  TRS B 232 1642   1577   3168   -531    171    120
> C
> HETATM 1805  C2  TRS B 232  37.795  -5.994  66.343  1.00 20.76
> C
> ANISOU 1805  C2  TRS B 232 2790   2021   3077 67    141   -408
> C
> HETATM 1806  C3  TRS B 232  38.160  -3.717  67.031  1.00 16.86
> C
> ANISOU 1806  C3  TRS B 232 2240   1557   2611   -491  8   -192
> C
> HETATM 1807  N   TRS B 232  38.227  -4.154  64.652  1.00 18.26
> N
> ANISOU 1807  N   TRS B 232 2336   2520   2083   -166 46   -112
> N
> HETATM 1808  O1  TRS B 232  40.741  -4.020  65.158  1.00 17.53
> O
> ANISOU 1808  O1  TRS B 232 1921   1579   3163   -225    147    197
> O
> HETATM 1809  O2  TRS B 232  37.871  -6.803  65.211  1.00 23.91
> O
> ANISOU 1809  O2  TRS B 232 3018   2456   3610    -48    -86   -450
> O
> HETATM 1810  O3  TRS B 232  38.871  -2.531  66.874  1.00 18.28
> O
> ANISOU 1810  O3  TRS B 232 2677   1594   2673    197 -4    -52
> O
>
> I get the output as the following file1.itp from your PRODRG server for TRS
> ligand before 3-4 months. I think this calculate is correct:
> file1.itp
> 
> [ moleculetype ]
> ; Name nrexcl
> TRS  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  TRS  O1 1   -0.240  15.9994
>  2    H  1  TRS HAA 1    0.052   1.0080
>  3   CH2 1  TRS  C1 1    0.061  14.0270
>  4   CH1 1  TRS   C 1    0.127  12.0110
>  5   CH2 1  TRS  C3 2    0.090  14.0270
>  6    OA 1  TRS  O3 2   -0.165  15.9994
>  7    H  1  TRS HAC 2    0.075   1.0080
>  8    NL 1  TRS   N 3    0.876  14.0067
>  9 H 1  TRS HAE 3    0.041   1.0080
>     10 H 1  TRS HAF 3    0.042   1.0080
>     11 H 1  TRS HAD 3    0.041   1.0080
>     12   CH2 1  TRS  C2 4    0.090  14.0270
>     13    OA 1  TRS  O2 4   -0.165  15.9994
>     14    H  1  TRS HAB 4    0.075   1.0080
> 
>
>
> But Now, That is, today,  I get the output as the following file2.itp from
> your PRODRG server for TRS ligand.
> file2.itp
> .
> [ moleculetype ]
> ; Name nrexcl
> TRS  3
>
> [ atoms ]
> ;   nr  type  resnr resid  atom  cgnr   charge mass
>  1    OA 1  TRS  O1 1   -0.173  15.9994
>  2 H 1  TRS H13 1    0.061   1.0080
>  3   CH2 1  TRS  C1 1    0.165  14.0270
>  4  CCL4 1  TRS   C 1    0.177  12.0110
>  5   CH2 1  TRS  C3 1    0.165  14.0270
>  6    OA 1  TRS  O3 1   -0.174  15.9994
>  7 H 1  TRS H33 1    0.062   1.0080
>  8    NL 1  TRS   N 1    0.675  14.0067
>  9 H 1  TRS  H2 1    0.014   1.0080
>     10 H 1  TRS  H3 1    0.014   1.0080
>     11 H 1  TRS  H1 1    0.014   1.0080
>     12   CH2 1  TRS  C2 2    0.144  14.0270
>     13    OA 1  TRS  O2 2   -0.198  15.9994
>     14 H 1  TRS H23 2    0.054   1.0080
> 
>
> Now, I think PRODRG calculate incorrectly  cgnr   charge
>
> What should I do? can you help me?
>
> --
> Ahmet YILDIRIM
>
> --
> gmx-users mailing list    gmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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Can't post? Re

[gmx-users] if PRODRG calculate incorrectly

[ahmet yıldırım]

Dear users,
I have a problem related to PRODRG.

Chirality:NO
Full charges: YES
Energy minimization: NO

*İnput file name:TRS.pdb*
HETATM 1803  C   TRS B 232  38.588  -4.733  65.956  1.00 17.99
C
ANISOU 1803  C   TRS B 232 2126   1948   2760   -378 45-81
C
HETATM 1804  C1  TRS B 232  40.103  -5.057  65.899  1.00 16.81
C
ANISOU 1804  C1  TRS B 232 1642   1577   3168   -531171120
C
HETATM 1805  C2  TRS B 232  37.795  -5.994  66.343  1.00 20.76
C
ANISOU 1805  C2  TRS B 232 2790   2021   3077 67141   -408
C
HETATM 1806  C3  TRS B 232  38.160  -3.717  67.031  1.00 16.86
C
ANISOU 1806  C3  TRS B 232 2240   1557   2611   -491  8   -192
C
HETATM 1807  N   TRS B 232  38.227  -4.154  64.652  1.00 18.26
N
ANISOU 1807  N   TRS B 232 2336   2520   2083   -166 46   -112
N
HETATM 1808  O1  TRS B 232  40.741  -4.020  65.158  1.00 17.53
O
ANISOU 1808  O1  TRS B 232 1921   1579   3163   -225147197
O
HETATM 1809  O2  TRS B 232  37.871  -6.803  65.211  1.00 23.91
O
ANISOU 1809  O2  TRS B 232 3018   2456   3610-48-86   -450
O
HETATM 1810  O3  TRS B 232  38.871  -2.531  66.874  1.00 18.28
O
ANISOU 1810  O3  TRS B 232 2677   1594   2673197 -4-52
O

I get the output *as the following file1.itp* from your PRODRG server for
TRS ligand before 3-4 months. I think this calculate is correct:
*file1.itp*

[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.240  15.9994
 2H  1  TRS HAA 10.052   1.0080
 3   CH2 1  TRS  C1 10.061  14.0270
 4   CH1 1  TRS   C 10.127  12.0110
 5   CH2 1  TRS  C3 20.090  14.0270
 6OA 1  TRS  O3 2   -0.165  15.9994
 7H  1  TRS HAC 20.075   1.0080
 8NL 1  TRS   N 30.876  14.0067
 9 H 1  TRS HAE 30.041   1.0080
10 H 1  TRS HAF 30.042   1.0080
11 H 1  TRS HAD 30.041   1.0080
12   CH2 1  TRS  C2 40.090  14.0270
13OA 1  TRS  O2 4   -0.165  15.9994
14H  1  TRS HAB 40.075   1.0080



But Now, That is, today,  I get the output *as the following file2.itp* from
your PRODRG server for TRS ligand.
*file2.itp*
.
[ moleculetype ]
; Name nrexcl
TRS  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  TRS  O1 1   -0.173  15.9994
 2 H 1  TRS H13 10.061   1.0080
 3   CH2 1  TRS  C1 10.165  14.0270
 4  CCL4 1  TRS   C 10.177  12.0110
 5   CH2 1  TRS  C3 10.165  14.0270
 6OA 1  TRS  O3 1   -0.174  15.9994
 7 H 1  TRS H33 10.062   1.0080
 8NL 1  TRS   N 10.675  14.0067
 9 H 1  TRS  H2 10.014   1.0080
10 H 1  TRS  H3 10.014   1.0080
11 H 1  TRS  H1 10.014   1.0080
12   CH2 1  TRS  C2 20.144  14.0270
13OA 1  TRS  O2 2   -0.198  15.9994
14 H 1  TRS H23 20.054   1.0080


Now, I think PRODRG calculate incorrectly  cgnr   charge

What should I do? can you help me?

-- 
Ahmet YILDIRIM
-- 
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