[gmx-users] gromos43a1p issue with ATP

Saman Shahriyari samanshahriyari at yahoo.com
Sat Jul 25 06:50:53 CEST 2015

Dear users

I am trying to run pdb2gmx on a protein holding ATP (with gromacs 467 and gromos43a1p.ff). However I have problem introducing ATP atom names in the input pdb file, based on the .rtp file of gromos43a1p (for example AO1PA is the name for an oxygen atom of ATP based on gromos43a1p .rtp. however pdb does not seem to know more than four characters for the atoms name and hence this pdb2gmx error prompts: atom AO1P was not found in .rtp ....). Can anyone gives me a clue on this?Regards,Saman


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