Farhan Ul Haq It will be more clear if you show share the screenshot of the error you have encountered. Anyway, in case of difference between the corrdinate files, see the number , if there is a difference of 3, increase the number of molecule by one in the top file. 2 for 6, 3 for 9 and so on. Normally you shoud not get such errors if you have performed the previous steps accurately.
Farhan Ul Haq It will be more clear if you show share the screenshot of the error you have encountered. Anyway, in case of difference between the corrdinate files, see the number , if there is a difference of 3, increase the number of molecule by one in the top file. 2 for 6, 3 for 9 and so on. Normally you shoud not get such errors if you have performed the previous steps accurately.
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro). At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number. Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file. Thank you.
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro). At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number. Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file. Thank you.
I had the same issue, here is the solution. Error: The number of coordinate files (22573) doesn't match the number in the topology files (22570). Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules. Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3. So, in my case i just increased one number and it worked. I increased the number of SOL molecules from 9336 to 9337. Good luck
I had the same issue, here is the solution. Error: The number of coordinate files (22573) doesn't match the number in the topology files (22570). Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules. Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3. So, in my case i just increased one number and it worked. I increased the number of SOL molecules from 9336 to 9337. Good luck
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro). At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number. Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file. Thank you.
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro). At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number. Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file. Thank you.
If you are sure on your chl.gro file after gmx pdb2gmx, I think you have to redo other steps again I remember I had the same problem but after making a new box everything was ok. (I checked your gro file and CHL molecule had some missing atoms)
If you are sure on your chl.gro file after gmx pdb2gmx, I think you have to redo other steps again I remember I had the same problem but after making a new box everything was ok. (I checked your gro file and CHL molecule had some missing atoms)
Hello everyone, I am getting the same issue but the issue is odd. I checked trough the pdb file and the gro file. the number of atoms is correct. however, the top file gives an error by two atoms. anybody else had the same issue? is there a system of adding some dummy atoms?
Hello everyone, I am getting the same issue but the issue is odd. I checked trough the pdb file and the gro file. the number of atoms is correct. however, the top file gives an error by two atoms. anybody else had the same issue? is there a system of adding some dummy atoms?
Hello everyone, In some cases, when you are doing work on Ligand-Protein Complex,, (SOL) solvent and ligand (drg) may be written in the same row in the Topol.top file. Modify the Topol.top file and upload it again.
Hello everyone, In some cases, when you are doing work on Ligand-Protein Complex,, (SOL) solvent and ligand (drg) may be written in the same row in the Topol.top file. Modify the Topol.top file and upload it again.
Hi,
open solv.gro and delete ligand entries after protein, change the number with topol.top, and run the command again.
Hi,
open solv.gro and delete ligand entries after protein, change the number with topol.top, and run the command again.
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@Ayesha Fatima you can use swiss pdb viewer tool to correct missing atoms
@Ayesha Fatima you can use swiss pdb viewer tool to correct missing atoms
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Farhan Ul Haq It will be more clear if you show share the screenshot of the error you have encountered. Anyway, in case of difference between the corrdinate files, see the number , if there is a difference of 3, increase the number of molecule by one in the top file. 2 for 6, 3 for 9 and so on. Normally you shoud not get such errors if you have performed the previous steps accurately.
Farhan Ul Haq It will be more clear if you show share the screenshot of the error you have encountered. Anyway, in case of difference between the corrdinate files, see the number , if there is a difference of 3, increase the number of molecule by one in the top file. 2 for 6, 3 for 9 and so on. Normally you shoud not get such errors if you have performed the previous steps accurately.
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If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).
At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.
Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.
Thank you.
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).
At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.
Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.
Thank you.
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hello everyone
how to solve this issue
"Reaction Preview Error Fixed atom coordinate mismatch. Fixed atom coordinates should match to within 0.0010"
hello everyone
how to solve this issue
"Reaction Preview Error Fixed atom coordinate mismatch. Fixed atom coordinates should match to within 0.0010"
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I had the same issue, here is the solution.
Error: The number of coordinate files (22573) doesn't match the number in the topology files (22570).
Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules.
Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3. So, in my case i just increased one number and it worked. I increased the number of SOL molecules from 9336 to 9337.
Good luck
I had the same issue, here is the solution.
Error: The number of coordinate files (22573) doesn't match the number in the topology files (22570).
Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules.
Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3. So, in my case i just increased one number and it worked. I increased the number of SOL molecules from 9336 to 9337.
Good luck
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VOTE
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).
At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.
Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.
Thank you.
If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).
At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.
Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.
Thank you.
More
VOTE
If you are sure on your chl.gro file after gmx pdb2gmx, I think you have to redo other steps again I remember I had the same problem but after making a new box everything was ok. (I checked your gro file and CHL molecule had some missing atoms)
If you are sure on your chl.gro file after gmx pdb2gmx, I think you have to redo other steps again I remember I had the same problem but after making a new box everything was ok. (I checked your gro file and CHL molecule had some missing atoms)
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VOTE
Hello everyone,
I am getting the same issue but the issue is odd. I checked trough the pdb file and the gro file. the number of atoms is correct. however, the top file gives an error by two atoms. anybody else had the same issue? is there a system of adding some dummy atoms?
Hello everyone,
I am getting the same issue but the issue is odd. I checked trough the pdb file and the gro file. the number of atoms is correct. however, the top file gives an error by two atoms. anybody else had the same issue? is there a system of adding some dummy atoms?
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Hello everyone,
In some cases, when you are doing work on Ligand-Protein Complex,, (SOL) solvent and ligand (drg) may be written in the same row in the Topol.top file. Modify the Topol.top file and upload it again.
Hello everyone,
In some cases, when you are doing work on Ligand-Protein Complex,, (SOL) solvent and ligand (drg) may be written in the same row in the Topol.top file. Modify the Topol.top file and upload it again.
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Hi people, I am facing this issue and I am unable to proceed, Any guidance will be appreciated :
Fatal error:
number of coordinates in coordinate file (solv.gro, 504056)
does not match topology (topol.top, 504058)
Aamir Mehmood In my case, the difference is of 2, Can you tell me whats the issue here ? Thanks
Hi people, I am facing this issue and I am unable to proceed, Any guidance will be appreciated :
Fatal error:
number of coordinates in coordinate file (solv.gro, 504056)
does not match topology (topol.top, 504058)
Aamir Mehmood In my case, the difference is of 2, Can you tell me whats the issue here ? Thanks
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