Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-16 Thread Mark Abraham 

On 16/04/2011 6:05 PM, ahmet yıldırım wrote:

Dear Justin,

I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for 
each EDO moleculeusing prodrg web server. Then I created 6 .itp files 
as EDO1.itp, EDO2.itp.EDO6.itp.


Why? The fragment

[molecules]
EDO 6

is what specifies six identical EDO molecules.

Your earlier problem was in matching the contents of your [molecules] 
section with your coordinate file. They have to contain the same 
molecules in the same order.


I changed residue numbers. But I have Fatal Error "moleculetype EDO is 
redefined". Am I on the wrong track?:-(


So don't re-define moleculetype EDO.

Mark



_*EDO1.itp:*_
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO  O1 1   -0.163  15.9994
 2H  1  EDO HAA 10.074   1.0080
 3   CH2 1  EDO  C1 10.089  14.0270
 4   CH2 1  EDO  C2 20.089  14.0270
 5OA 1  EDO  O2 2   -0.163  15.9994
 6H  1  EDO HAB 20.074   1.0080

*_EDO2.itp:_*
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 2  EDO  O1 1   -0.163  15.9994
 2H2  EDO HAA 10.074   1.0080
 3   CH2 2  EDO  C1 10.089  14.0270
 4   CH2 2  EDO  C2 20.089  14.0270
 5OA 2  EDO  O2 2   -0.163  15.9994
 6H2  EDO HAB 20.074   1.0080
_*topol.top*_:
...
#include "EDO1.itp"
#include "EDO2.itp"
#include "EDO3.itp"
#include "EDO4.itp"
#include "EDO5.itp"
#include "EDO6.itp"
#include "TRS.itp"
...
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
EDO 6
TRS 1
SOL   185
SOL   143
SOL 33713

_*conf.gro:*_
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5384
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763


  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  O1   1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  C1   3   0.596  -3.211  -0.163
1EDO  C2   4   0.486  -3.247  -0.261
1EDO  O2   5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
2EDO  O1   1   2.023  -4.300   0.220
2EDO  HAA  2   2.046  -4.296   0.317
2EDO  C1   3   2.138  -4.342   0.146
2EDO  C2   4   2.096  -4.347  -0.001
2EDO  O2   5   2.196  -4.412  -0.079
2EDO  HAB  6   2.167  -4.415  -0.174
3EDO  O1   1   2.502  -3.407  -2.265
3EDO  HAA  2   2.529  -3.365  -2.178
3EDO  C1   3   2.466  -3.303  -2.359
3EDO  C2   4   2.424  -3.364  -2.492
3EDO  O2   5   2.294  -3.423  -2.477
3EDO  HAB  6   2.265  -3.464  -2.564
4EDO  O1   1   1.021  -5.733  -2.007
4EDO  HAA  2   0.952  -5.780  -2.061
4EDO  C1   3   0.995  -5.753  -1.868
4EDO  C2   4   1.102  -5.679  -1.787
4EDO  O2   5   1.091  -5.540  -1.816
4EDO  HAB  6   1.160  -5.489  -1.764
5EDO  O1   1   1.988  -3.117  -3.247
5EDO  HAA  2   1.915  -3.177  -3.217
5EDO  C1   3   2.100  -3.194  -3.291
5EDO  C2   4   2.212  -3.102  -3.337
5EDO  O2   5   2.247  -3.012  -3.231
5EDO  HAB  6   2.321  -2.952  -3.261
6EDO  O1   1   0.987  -4.579  -0.020
6EDO  HAA  2   0.969  -4.622  -0.109
6EDO  C1   3   1.118  -4.521  -0.021
6EDO  C2   4   1.145  -4.456   0.114
6EDO  O2   5   1.054  -4.506   0.212
6EDO  HAB  6   1.073  -4.463   0.300
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   
0.0   0.0   0.0


14 Nisan 2011 21:09 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear Justin,

Thanks for your valuable helps. How should I rearranged the
conf.gro file for 6 EDO ligand?  is the following conf.gro
mistake?


Well, it's certainly not working, is it?  You only have one EDO
molecule shown here.  Is this the only one?  If it is, then you

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-16 Thread ahmet yıldırım 
Dear Justin,

I have 6 EDO and 1 TRS ligans. I created coordinate and .itp files for eachEDO
molecule using prodrg web server. Then I created 6 .itp files as EDO1.itp,
EDO2.itp.EDO6.itp. I changed residue numbers. But I have Fatal Error
"moleculetype EDO is redefined". Am I on the wrong track?:-(

*EDO1.itp:*
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 1  EDO  O1 1   -0.163  15.9994
 2H  1  EDO HAA 10.074   1.0080
 3   CH2 1  EDO  C1 10.089  14.0270
 4   CH2 1  EDO  C2 20.089  14.0270
 5OA 1  EDO  O2 2   -0.163  15.9994
 6H  1  EDO HAB 20.074   1.0080

*EDO2.itp:*
[ moleculetype ]
; Name nrexcl
EDO  3

[ atoms ]
;   nr  type  resnr resid  atom  cgnr   charge mass
 1OA 2  EDO  O1 1   -0.163  15.9994
 2H2  EDO HAA 10.074   1.0080
 3   CH2 2  EDO  C1 10.089  14.0270
 4   CH2 2  EDO  C2 20.089  14.0270
 5OA 2  EDO  O2 2   -0.163  15.9994
 6H2  EDO HAB 20.074   1.0080
*topol.top*:
...
#include "EDO1.itp"
#include "EDO2.itp"
#include "EDO3.itp"
#include "EDO4.itp"
#include "EDO5.itp"
#include "EDO6.itp"
#include "TRS.itp"
...
[ molecules ]
; Compound#mols
Protein_chain_A 1
Protein_chain_B 1
EDO 6
TRS 1
SOL   185
SOL   143
SOL 33713

*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5384
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763


  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  O1   1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  C1   3   0.596  -3.211  -0.163
1EDO  C2   4   0.486  -3.247  -0.261
1EDO  O2   5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
2EDO  O1   1   2.023  -4.300   0.220
2EDO  HAA  2   2.046  -4.296   0.317
2EDO  C1   3   2.138  -4.342   0.146
2EDO  C2   4   2.096  -4.347  -0.001
2EDO  O2   5   2.196  -4.412  -0.079
2EDO  HAB  6   2.167  -4.415  -0.174
3EDO  O1   1   2.502  -3.407  -2.265
3EDO  HAA  2   2.529  -3.365  -2.178
3EDO  C1   3   2.466  -3.303  -2.359
3EDO  C2   4   2.424  -3.364  -2.492
3EDO  O2   5   2.294  -3.423  -2.477
3EDO  HAB  6   2.265  -3.464  -2.564
4EDO  O1   1   1.021  -5.733  -2.007
4EDO  HAA  2   0.952  -5.780  -2.061
4EDO  C1   3   0.995  -5.753  -1.868
4EDO  C2   4   1.102  -5.679  -1.787
4EDO  O2   5   1.091  -5.540  -1.816
4EDO  HAB  6   1.160  -5.489  -1.764
5EDO  O1   1   1.988  -3.117  -3.247
5EDO  HAA  2   1.915  -3.177  -3.217
5EDO  C1   3   2.100  -3.194  -3.291
5EDO  C2   4   2.212  -3.102  -3.337
5EDO  O2   5   2.247  -3.012  -3.231
5EDO  HAB  6   2.321  -2.952  -3.261
6EDO  O1   1   0.987  -4.579  -0.020
6EDO  HAA  2   0.969  -4.622  -0.109
6EDO  C1   3   1.118  -4.521  -0.021
6EDO  C2   4   1.145  -4.456   0.114
6EDO  O2   5   1.054  -4.506   0.212
6EDO  HAB  6   1.073  -4.463   0.300
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
0.0   0.0

14 Nisan 2011 21:09 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> Thanks for your valuable helps. How should I rearranged the conf.gro file
>> for 6 EDO ligand?  is the following conf.gro mistake?
>>
>>
> Well, it's certainly not working, is it?  You only have one EDO molecule
> shown here.  Is this the only one?  If it is, then you need to build the
> system to reflect what you actually want to do.  No one on this list can
> tell you that. You have to build a starting configuration that fits the
> goals of your study.
>
> -Justin
>
>  _*conf.gro:*_
>>
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>>  5354
>>2GLN  N1   1.458  -1.158   0.739
>>2GLN H12   1.520  -1.083   0.763
>> ...
>>  485HOHHW1 5333   0.221  -3.8

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread Justin A. Lemkul 



ahmet yıldırım wrote:

Dear Justin,

Thanks for your valuable helps. How should I rearranged the conf.gro 
file for 6 EDO ligand?  is the following conf.gro mistake?




Well, it's certainly not working, is it?  You only have one EDO molecule shown 
here.  Is this the only one?  If it is, then you need to build the system to 
reflect what you actually want to do.  No one on this list can tell you that. 
You have to build a starting configuration that fits the goals of your study.


-Justin


_*conf.gro:*_
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  OAB  1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  CAA  3   0.596  -3.211  -0.163
1EDO  CAC  4   0.486  -3.247  -0.261
1EDO  OAD  5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222

   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0   
0.0   0.0


14 Nisan 2011 20:15 tarihinde Justin A. Lemkul > yazdı:




ahmet yıldırım wrote:

Dear Justin,

I built .rtp entries for two ligands using
(http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the
topol.top the following parts:
#include "TRS.itp"
#include "EDO.itp"


Well, either pdb2gmx built the molecules into your topology or
you're #including them in this manner, you should not do both.

TRS 1
EDO 6


So this is part of your [molecules] directive?  If you've got six
copies of EDO, that's likely where the disconnect comes from - you
only had one in your previous coordinate file snippet.


Furthermore I added the number of atoms (20) in the second line
of the


If you have 6 EDO, the necessary addition is more than just 20.


.gro file. may the problem related to pdb file (3NM4.pdb)?
Because  -OH groups seems as -O. isn't it? maybe I'm wrong. What
would you recommend?


Generally H atoms are not present in crystal structures.  If your
ligands require certain H atoms, then you must do one of two things:

1. Add all the necessary hydrogen atoms to the protein and ligands
and run pdb2gmx.

2. Have no H atoms present in the initial coordinate file and build
suitable .hdb entries for your ligands so they will be constructed
from existing atoms.

It seems like you're applying several different methods at once.
 There are protein-ligand tutorials that you may find useful for
keeping all of this straight (I recommend my own):

http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems

-Justin

2011/4/14 Justin A. Lemkul mailto:jalem...@vt.edu> >>




   ahmet yıldırım wrote:

   Dear users,

   pdb2gmx -f xxx.pdb
   water:spc
   forcefield:43a1
   editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
   genbox -cp box.gro -cs spc216.gro -p topol.top -o
solvated.gro
   grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
   *Fatal error:*
   number of coordinates in coordinate file (solvated.gro,
106523)
   does not match topology (topol.top, 106553)
   I look at gmx-user search. But I dont be able to solved the
   problem. Then I look at conf.gro and box.gro. I
recognised the
   there is not the TRS ligand in the box.gro file. What reason?


   Based on your workflow, it looks as is you never added it in.  If
   conf.gro came from pdb2gmx, did you build .rtp entries for your
   ligands, or just #include .itp files after the fact?  If the
latter,
   then you have to modify the coordinate file (conf.gro) to include
   these molecules.  If you did this but did not correctly increment
   the number of atoms in the second line of the .gro file, likely
   anything with a higher atom number got truncated.  If the
conf.gro
   file you show below is

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread ahmet yıldırım 
Dear Justin,

Thanks for your valuable helps. How should I rearranged the conf.gro file
for 6 EDO ligand?  is the following conf.gro mistake?

*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  OAB  1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  CAA  3   0.596  -3.211  -0.163
1EDO  CAC  4   0.486  -3.247  -0.261
1EDO  OAD  5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222

   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
0.0   0.0

14 Nisan 2011 20:15 tarihinde Justin A. Lemkul  yazdı:

>
>
> ahmet yıldırım wrote:
>
>> Dear Justin,
>>
>> I built .rtp entries for two ligands using (
>> http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the
>> following parts:
>> #include "TRS.itp"
>> #include "EDO.itp"
>>
>
> Well, either pdb2gmx built the molecules into your topology or you're
> #including them in this manner, you should not do both.
>
>  TRS 1
>> EDO 6
>>
>
> So this is part of your [molecules] directive?  If you've got six copies of
> EDO, that's likely where the disconnect comes from - you only had one in
> your previous coordinate file snippet.
>
>
>  Furthermore I added the number of atoms (20) in the second line of the
>>
>
> If you have 6 EDO, the necessary addition is more than just 20.
>
>
>  .gro file. may the problem related to pdb file (3NM4.pdb)? Because  -OH
>> groups seems as -O. isn't it? maybe I'm wrong. What would you recommend?
>>
>>
> Generally H atoms are not present in crystal structures.  If your ligands
> require certain H atoms, then you must do one of two things:
>
> 1. Add all the necessary hydrogen atoms to the protein and ligands and run
> pdb2gmx.
>
> 2. Have no H atoms present in the initial coordinate file and build
> suitable .hdb entries for your ligands so they will be constructed from
> existing atoms.
>
> It seems like you're applying several different methods at once.  There are
> protein-ligand tutorials that you may find useful for keeping all of this
> straight (I recommend my own):
>
> http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems
>
> -Justin
>
>  2011/4/14 Justin A. Lemkul mailto:jalem...@vt.edu>>
>>
>>
>>
>>
>>ahmet yıldırım wrote:
>>
>>Dear users,
>>
>>pdb2gmx -f xxx.pdb
>>water:spc
>>forcefield:43a1
>>editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
>>genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>>grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>>*Fatal error:*
>>number of coordinates in coordinate file (solvated.gro, 106523)
>>does not match topology (topol.top, 106553)
>>I look at gmx-user search. But I dont be able to solved the
>>problem. Then I look at conf.gro and box.gro. I recognised the
>>there is not the TRS ligand in the box.gro file. What reason?
>>
>>
>>Based on your workflow, it looks as is you never added it in.  If
>>conf.gro came from pdb2gmx, did you build .rtp entries for your
>>ligands, or just #include .itp files after the fact?  If the latter,
>>then you have to modify the coordinate file (conf.gro) to include
>>these molecules.  If you did this but did not correctly increment
>>the number of atoms in the second line of the .gro file, likely
>>anything with a higher atom number got truncated.  If the conf.gro
>>file you show below is indeed what you used, though, I see no reason
>>why this should have happened except that perhaps you left out a
>>step you thought you had done previously.
>>
>>The difference in the coordinate file vs. topology is 30 atoms,
>>which is more than both of your ligands (20 atoms), so your problem
>>likely lies elsewhere.
>>
>>-Justin
>>
>>
>>Thanks in advance
>>
>>_*conf.gro:*_
>>MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>> 5354
>>   2GLN  N1   1.458  -1.158   0.739
>>   2GLN H12   1.520  -1.083   0.763
>>...
>> 485HOHHW1 5333   0.221  -3.864  -2.291
>>

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread Justin A. Lemkul 



ahmet yıldırım wrote:

Dear Justin,

I built .rtp entries for two ligands using 
(http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top 
the following parts:

#include "TRS.itp"
#include "EDO.itp"


Well, either pdb2gmx built the molecules into your topology or you're #including 
them in this manner, you should not do both.



TRS 1
EDO 6


So this is part of your [molecules] directive?  If you've got six copies of EDO, 
that's likely where the disconnect comes from - you only had one in your 
previous coordinate file snippet.


Furthermore I added the number of atoms (20) in the second line of the 


If you have 6 EDO, the necessary addition is more than just 20.

.gro file. may the problem related to pdb file (3NM4.pdb)? Because  -OH 
groups seems as -O. isn't it? maybe I'm wrong. What would you recommend?




Generally H atoms are not present in crystal structures.  If your ligands 
require certain H atoms, then you must do one of two things:


1. Add all the necessary hydrogen atoms to the protein and ligands and run 
pdb2gmx.

2. Have no H atoms present in the initial coordinate file and build suitable 
.hdb entries for your ligands so they will be constructed from existing atoms.


It seems like you're applying several different methods at once.  There are 
protein-ligand tutorials that you may find useful for keeping all of this 
straight (I recommend my own):


http://www.gromacs.org/Documentation/Tutorials#Protein-Ligand_Systems

-Justin


2011/4/14 Justin A. Lemkul mailto:jalem...@vt.edu>>



ahmet yıldırım wrote:

Dear users,

pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordinate file (solvated.gro, 106523)
does not match topology (topol.top, 106553)
I look at gmx-user search. But I dont be able to solved the
problem. Then I look at conf.gro and box.gro. I recognised the
there is not the TRS ligand in the box.gro file. What reason?


Based on your workflow, it looks as is you never added it in.  If
conf.gro came from pdb2gmx, did you build .rtp entries for your
ligands, or just #include .itp files after the fact?  If the latter,
then you have to modify the coordinate file (conf.gro) to include
these molecules.  If you did this but did not correctly increment
the number of atoms in the second line of the .gro file, likely
anything with a higher atom number got truncated.  If the conf.gro
file you show below is indeed what you used, though, I see no reason
why this should have happened except that perhaps you left out a
step you thought you had done previously.

The difference in the coordinate file vs. topology is 30 atoms,
which is more than both of your ligands (20 atoms), so your problem
likely lies elsewhere.

-Justin


Thanks in advance

_*conf.gro:*_
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
   2GLN  N1   1.458  -1.158   0.739
   2GLN H12   1.520  -1.083   0.763
...
 485HOHHW1 5333   0.221  -3.864  -2.291
 485HOHHW2 5334   0.303  -3.946  -2.407
   1EDO  OAB  1   0.625  -3.071  -0.171
   1EDO  HAA  2   0.698  -3.048  -0.107
   1EDO  CAA  3   0.596  -3.211  -0.163
   1EDO  CAC  4   0.486  -3.247  -0.261
   1EDO  OAD  5   0.365  -3.179  -0.224
   1EDO  HAB  6   0.292  -3.203  -0.288
   1TRS  O1   1   1.825  -3.900   0.047
   1TRS  HAA  2   1.853  -3.860  -0.040
   1TRS  C1   3   1.712  -3.977   0.028
   1TRS  C4   1.659  -4.044   0.150
   1TRS  C3   5   1.576  -3.946   0.226
   1TRS  O3   6   1.634  -3.824   0.256
   1TRS  HAC  7   1.569  -3.768   0.307
   1TRS  N8   1.582  -4.159   0.113
   1TRS  HAE  9   1.547  -4.204   0.195
   1TRS  HAF 10   1.505  -4.131   0.056
   1TRS  HAD 11   1.639  -4.223   0.062
   1TRS  C2  12   1.776  -4.085   0.233
   1TRS  O2  13   1.887  -4.122   0.160
   1TRS  HAB 14   1.961  -4.148   0.222
  8.13100   7.04165  13.54850   0.0   0.0  -4.06550  
0.0   0.0   0.0






-- 
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

==

Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread ahmet yıldırım 
Dear Justin,

I built .rtp entries for two ligands using (
http://davapc1.bioch.dundee.ac.uk/prodrg/). I added to the topol.top the
following parts:
#include "TRS.itp"
#include "EDO.itp"
TRS 1
EDO 6
Furthermore I added the number of atoms (20) in the second line of the .gro
file. may the problem related to pdb file (3NM4.pdb)? Because  -OH groups
seems as -O. isn't it? maybe I'm wrong. What would you recommend?

2011/4/14 Justin A. Lemkul 

>
>
> ahmet yıldırım wrote:
>
>> Dear users,
>>
>> pdb2gmx -f xxx.pdb
>> water:spc
>> forcefield:43a1
>> editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
>> genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
>> grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>> *Fatal error:*
>> number of coordinates in coordinate file (solvated.gro, 106523) does not
>> match topology (topol.top, 106553)
>> I look at gmx-user search. But I dont be able to solved the problem. Then
>> I look at conf.gro and box.gro. I recognised the there is not the TRS ligand
>> in the box.gro file. What reason?
>>
>>
> Based on your workflow, it looks as is you never added it in.  If conf.gro
> came from pdb2gmx, did you build .rtp entries for your ligands, or just
> #include .itp files after the fact?  If the latter, then you have to modify
> the coordinate file (conf.gro) to include these molecules.  If you did this
> but did not correctly increment the number of atoms in the second line of
> the .gro file, likely anything with a higher atom number got truncated.  If
> the conf.gro file you show below is indeed what you used, though, I see no
> reason why this should have happened except that perhaps you left out a step
> you thought you had done previously.
>
> The difference in the coordinate file vs. topology is 30 atoms, which is
> more than both of your ligands (20 atoms), so your problem likely lies
> elsewhere.
>
> -Justin
>
>
>  Thanks in advance
>>
>> _*conf.gro:*_
>> MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
>>  5354
>>2GLN  N1   1.458  -1.158   0.739
>>2GLN H12   1.520  -1.083   0.763
>> ...
>>  485HOHHW1 5333   0.221  -3.864  -2.291
>>  485HOHHW2 5334   0.303  -3.946  -2.407
>>1EDO  OAB  1   0.625  -3.071  -0.171
>>1EDO  HAA  2   0.698  -3.048  -0.107
>>1EDO  CAA  3   0.596  -3.211  -0.163
>>1EDO  CAC  4   0.486  -3.247  -0.261
>>1EDO  OAD  5   0.365  -3.179  -0.224
>>1EDO  HAB  6   0.292  -3.203  -0.288
>>1TRS  O1   1   1.825  -3.900   0.047
>>1TRS  HAA  2   1.853  -3.860  -0.040
>>1TRS  C1   3   1.712  -3.977   0.028
>>1TRS  C4   1.659  -4.044   0.150
>>1TRS  C3   5   1.576  -3.946   0.226
>>1TRS  O3   6   1.634  -3.824   0.256
>>1TRS  HAC  7   1.569  -3.768   0.307
>>1TRS  N8   1.582  -4.159   0.113
>>1TRS  HAE  9   1.547  -4.204   0.195
>>1TRS  HAF 10   1.505  -4.131   0.056
>>1TRS  HAD 11   1.639  -4.223   0.062
>>1TRS  C2  12   1.776  -4.085   0.233
>>1TRS  O2  13   1.887  -4.122   0.160
>>1TRS  HAB 14   1.961  -4.148   0.222
>>   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
>> 0.0   0.0
>>
>>
>>
>>
>>
>> --
>> 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 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/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
>



-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread Justin A. Lemkul 



ahmet yıldırım wrote:

Dear users,

pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordinate file (solvated.gro, 106523) does not 
match topology (topol.top, 106553)
I look at gmx-user search. But I dont be able to solved the problem. 
Then I look at conf.gro and box.gro. I recognised the there is not the 
TRS ligand in the box.gro file. What reason?




Based on your workflow, it looks as is you never added it in.  If conf.gro came 
from pdb2gmx, did you build .rtp entries for your ligands, or just #include .itp 
files after the fact?  If the latter, then you have to modify the coordinate 
file (conf.gro) to include these molecules.  If you did this but did not 
correctly increment the number of atoms in the second line of the .gro file, 
likely anything with a higher atom number got truncated.  If the conf.gro file 
you show below is indeed what you used, though, I see no reason why this should 
have happened except that perhaps you left out a step you thought you had done 
previously.


The difference in the coordinate file vs. topology is 30 atoms, which is more 
than both of your ligands (20 atoms), so your problem likely lies elsewhere.


-Justin


Thanks in advance

_*conf.gro:*_
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  OAB  1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  CAA  3   0.596  -3.211  -0.163
1EDO  CAC  4   0.486  -3.247  -0.261
1EDO  OAD  5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0   
0.0   0.0






--
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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[gmx-users] Fatal error: number of coordinates in coordinate file does not match topology

2011-04-14 Thread ahmet yıldırım 
Dear users,

pdb2gmx -f xxx.pdb
water:spc
forcefield:43a1
editconf -f conf.gro -bt cubic -d 1.0 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
*Fatal error:*
number of coordinates in coordinate file (solvated.gro, 106523) does not
match topology (topol.top, 106553)
I look at gmx-user search. But I dont be able to solved the problem. Then I
look at conf.gro and box.gro. I recognised the there is not the TRS ligand
in the box.gro file. What reason?

Thanks in advance

*conf.gro:*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
 5354
2GLN  N1   1.458  -1.158   0.739
2GLN H12   1.520  -1.083   0.763
...
  485HOHHW1 5333   0.221  -3.864  -2.291
  485HOHHW2 5334   0.303  -3.946  -2.407
1EDO  OAB  1   0.625  -3.071  -0.171
1EDO  HAA  2   0.698  -3.048  -0.107
1EDO  CAA  3   0.596  -3.211  -0.163
1EDO  CAC  4   0.486  -3.247  -0.261
1EDO  OAD  5   0.365  -3.179  -0.224
1EDO  HAB  6   0.292  -3.203  -0.288
1TRS  O1   1   1.825  -3.900   0.047
1TRS  HAA  2   1.853  -3.860  -0.040
1TRS  C1   3   1.712  -3.977   0.028
1TRS  C4   1.659  -4.044   0.150
1TRS  C3   5   1.576  -3.946   0.226
1TRS  O3   6   1.634  -3.824   0.256
1TRS  HAC  7   1.569  -3.768   0.307
1TRS  N8   1.582  -4.159   0.113
1TRS  HAE  9   1.547  -4.204   0.195
1TRS  HAF 10   1.505  -4.131   0.056
1TRS  HAD 11   1.639  -4.223   0.062
1TRS  C2  12   1.776  -4.085   0.233
1TRS  O2  13   1.887  -4.122   0.160
1TRS  HAB 14   1.961  -4.148   0.222
   8.13100   7.04165  13.54850   0.0   0.0  -4.06550   0.0
0.0   0.0





-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

2008-10-11 Thread Tsjerk Wassenaar 
Hi Chitrita,

Please copy-paste the exact error and the command line in both cases
(working and not working). Also, what platform are you working on? Did
you by chance edit the .mdp file under windows?

Cheers,

Tsjerk

On Sat, Oct 11, 2008 at 6:46 PM, Chitrita Dutta Roy
<[EMAIL PROTECTED]> wrote:
> I want to perform MD Equilibration run under position restrained for 200ps.
> Bond distances were constrained using the LINCS (Linear Constraints)
> algorithm, the water molecules were restrained using the SETTLE algorithm.
> In order to do this I have modified nsteps in original pr.mdp file.
> Following is the modified file contents:
>
>
>
> ;
>
> ; User spoel (236)
>
> ; Wed Nov 3 17:12:44 1993
>
> ; Input file
>
> ;
>
> title = Yo
>
> cpp = /usr/bin/cpp
>
> define = -DPOSRES
>
> constraints = all-bonds
>
> integrator = md
>
> dt = 0.002 ; ps !
>
> nsteps = 10 ; total 200 ps.
>
> nstcomm = 1
>
> nstxout = 50
>
> nstvout = 1000
>
> nstfout = 0
>
> nstlog = 10
>
> nstenergy = 10
>
> nstlist = 10
>
> ns_type = grid
>
> rlist = 1.0
>
> rcoulomb = 1.0
>
> rvdw = 1.0
>
> ; Berendsen temperature coupling is on in two groups
>
> Tcoupl = berendsen
>
> tc-grps = Protein SOL
>
> tau_t = 0.1 0.1
>
> ref_t = 300 300
>
> ; Energy monitoring
>
> energygrps = Protein SOL
>
> ; Pressure coupling is not on
>
> Pcoupl = no
>
> tau_p = 0.5
>
> compressibility = 4.5e-5
>
> ref_p = 1.0
>
> ; Generate velocites is on at 300 K.
>
> gen_vel = yes
>
> gen_temp = 300.0
>
> gen_seed = 173529
>
>
>
> Then I wanted to do grompp with this modified pr.mdp file. But it is showing
> a Fatal error like,
>
> Fatal Error:
>
> number of coordinates in coordinate file does not match topology.
>
> But if I use the original pr.mdp (without modifying it for 200ps) the grompp
> runs properly. I am not understanding what to do now. Please help me out.
>
> Thanking you,
>
> Chitrita.
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to [EMAIL PROTECTED]
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>



-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
___
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[gmx-users] Fatal Error: number of coordinates in coordinate file does not match topology

2008-10-11 Thread Chitrita Dutta Roy 
I want to perform MD Equilibration run under position restrained for
200ps. Bond
distances were constrained using the LINCS (Linear Constraints) algorithm,
the water molecules were restrained using the SETTLE algorithm. In order to
do this I have modified nsteps in original pr.mdp file. Following is the
modified file contents:



;

; User spoel (236)

; Wed Nov 3 17:12:44 1993

; Input file

;

title = Yo

cpp = /usr/bin/cpp

define = -DPOSRES

constraints = all-bonds

integrator = md

dt = 0.002 ; ps !

nsteps = 10 ; total 200 ps.

nstcomm = 1

nstxout = 50

nstvout = 1000

nstfout = 0

nstlog = 10

nstenergy = 10

nstlist = 10

ns_type = grid

rlist = 1.0

rcoulomb = 1.0

rvdw = 1.0

; Berendsen temperature coupling is on in two groups

Tcoupl = berendsen

tc-grps = Protein SOL

tau_t = 0.1 0.1

ref_t = 300 300

; Energy monitoring

energygrps = Protein SOL

; Pressure coupling is not on

Pcoupl = no

tau_p = 0.5

compressibility = 4.5e-5

ref_p = 1.0

; Generate velocites is on at 300 K.

gen_vel = yes

gen_temp = 300.0

gen_seed = 173529



Then I wanted to do grompp with this modified pr.mdp file. But it is showing
a Fatal error like,

Fatal Error:

number of coordinates in coordinate file does not match topology.

But if I use the original pr.mdp (without modifying it for 200ps) the grompp
runs properly. I am not understanding what to do now. Please help me out.

Thanking you,

Chitrita.
___
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Please search the archive at http://www.gromacs.org/search before posting!
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