normal Topology problem with atom2cg and seq2itp scripts

  • edroaldo
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12 years 6 months ago #792 by edroaldo
Dear MARTINI users, I have a problem with the names generated by the atom2cg and seq2itp scripts when I try to follow the tutorial in the MARTINI web site. The atom names generated by atom2cg int the .pdb file are, for example, BB, S1, BB, S2... and the atom names generated to seq2itp are BBc, S1c, BBe, S1e and so on and when I run grompp I get the following errors:
Warning: atom name 1 in system.top and 1ubqcg.pdb does not match (BBc - BB)
Warning: atom name 2 in system.top and 1ubqcg.pdb does not match (S1c - S1)
Warning: atom name 3 in system.top and 1ubqcg.pdb does not match (BBe - BB)
Warning: atom name 4 in system.top and 1ubqcg.pdb does not match (S1e - S1)
Warning: atom name 5 in system.top and 1ubqcg.pdb does not match (BBe - BB)
I download the scripts from MARTINI web site. What is wrong? Can you please help me?

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12 years 6 months ago #793 by edroaldo
Problem solved, I do search in this mailing list and now I find the answer. I searched before but I did not find anything. The post that I found to solve the problem is:
md.chem.rug.nl/cgmartini/index.php/user-...rm/forum/topic?id=63
Sorry for this question.

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12 years 6 months ago #794 by djurre
dear edroaldo,

As the Warning message states, there is a difference in atom names:
The name in the top file is 'BBc' while for the same bead in the gro file it is 'BB'. This is just a naming difference (the 'c' specifies the secondary structure type). Gromacs will use the name in the top file, which is fine.

Now, knowing that this error is nothing very serious, you can set the grompp options '-maxwarn 1'. It will ignore this warning (if there are more warnings AND you have made sure these are nothing serious either you have to set the maxwarn higher).

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