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<p>I'm fully aware that this is a forum for discussing Gromacs, but there's a bit of a frustrating situation that involves using it.</p>
<p>I need a linear ssDNA chain, sequence of my choosing, anything that will work with, say, AMBER99SB-ILDN. Not trying to find any funny forcefields for it, everything as is. You suggested AMBER in the past, so AMBER it is.</p>
<p><br></p>
<p>ChemOffice produced a PDB with incompatible atom types. make-na server (http://structure.usc.edu/make-na/server.html) also produced something pdb2gmx hates. Is there absolutely any way to get a PDB that will produce a usable topology out of the box with an established potential implemented in Gromacs? Anything that will not involve manual modification of PDBs or writing text-processing scripts will make me very happy.</p>
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<p>I will really appreciate any suggestions.</p>
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<p>Thank you,</p>
<p><br></p>
<p>Alex</p>
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