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problems with topology/ simulation
- meher
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14 years 2 weeks ago #345
by meher
problems with topology/ simulation was created by meher
The problem is now solved. It was twofold: firstly I had to change the vdwd as suggested and after this I got a LINCS error with the protein exploding. then I ran a simulation with position restraints as suggested in the tutorial - with all protein atoms constrained and then just the backbone atoms constrained. Now the protein seems to be happy.
many thanks
meher
>> I was trying to run a simulation of a protein using the Martiini force fields in Gromacs. However, I have encountered the following errors so far, and could not proceed further. Any help you could provide is greatly appreciated. Many thanks in advance!
> Please try to use the Martini User Forum at www.cgmartini.nl/index.php/forum for these kind of questions so everybody can benefit from the advise.
>> 1. I created the coarse grained pdb and the itp files for the protein. In the making of the tpr using grompp, it crashed with a warning:
>> processing coordinates...
>> Warning: atom name 1 in SecA.top and CG.pdb does not match (BCQd - BN0)
>> Warning: atom name 2 in SecA.top and CG.pdb does not match (SCAC2 - SC1)
>> Warning: atom name 3 in SecA.top and CG.pdb does not match (BCP5 - BN0)
> The atom names in the .gro don't matter, only atom types in the topology matter. Ignore the warning.
>> 2. I ignored the warning on the grompp with -maxwarn 5 . However, when I used the resulting tpr with mdrun, it crashed immediately with the following error:
>>
>> Wrote pdb files with previous and current coordinates
>> There were 96 inconsistent shifts. Check your topology
>>
>> I need help figuring out if problem #1 I had resulted in #2 or if these are two independent problems and how to deal with them. Please let me know if any other information is needed,
>> -meher
> They are independent problems, but the error message is not enough to say what's wrong. Maybe you have overlapping atoms in the system? Did you minimise and use genbox with -vdwd 0.24?
> -martti-
many thanks
meher
>> I was trying to run a simulation of a protein using the Martiini force fields in Gromacs. However, I have encountered the following errors so far, and could not proceed further. Any help you could provide is greatly appreciated. Many thanks in advance!
> Please try to use the Martini User Forum at www.cgmartini.nl/index.php/forum for these kind of questions so everybody can benefit from the advise.
>> 1. I created the coarse grained pdb and the itp files for the protein. In the making of the tpr using grompp, it crashed with a warning:
>> processing coordinates...
>> Warning: atom name 1 in SecA.top and CG.pdb does not match (BCQd - BN0)
>> Warning: atom name 2 in SecA.top and CG.pdb does not match (SCAC2 - SC1)
>> Warning: atom name 3 in SecA.top and CG.pdb does not match (BCP5 - BN0)
> The atom names in the .gro don't matter, only atom types in the topology matter. Ignore the warning.
>> 2. I ignored the warning on the grompp with -maxwarn 5 . However, when I used the resulting tpr with mdrun, it crashed immediately with the following error:
>>
>> Wrote pdb files with previous and current coordinates
>> There were 96 inconsistent shifts. Check your topology
>>
>> I need help figuring out if problem #1 I had resulted in #2 or if these are two independent problems and how to deal with them. Please let me know if any other information is needed,
>> -meher
> They are independent problems, but the error message is not enough to say what's wrong. Maybe you have overlapping atoms in the system? Did you minimise and use genbox with -vdwd 0.24?
> -martti-
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