Hi there,<div><br></div><div>Is there an option in pdb2gmx that when generating the top/itp file, it could show the parameters explicitly? e.g.:</div><div><br></div><div>Instead of:</div><div><div>[ dihedrals ]</div><div>; ai aj ak al funct c0 c1 c2 c3</div>
<div> 5 13 11 12 4 </div><div> 11 15 13 14 4 </div><div> 15 23 21 22 4 </div><div> 21 25 23 24 4 </div><div> 25 32 31 33 4 </div><div><br></div>
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(my hard hand modifications)</div><div><br></div><div><div>[ dihedrals ] ; impropers</div><div>; treated as propers in GROMACS to use correct AMBER analytical function</div><div>; i j k l func phase kd pn</div>
<div> 5 13 11 12 4 180.00 43.93200 2 ; CA- N- C- O</div><div> 11 15 13 14 4 180.00 4.60240 2 ; C- CA- N- H</div><div> 15 23 21 22 4 180.00 43.93200 2 ; CA- N- C- O</div>
<div> 21 25 23 24 4 180.00 4.60240 2 ; C- CA- N- H</div><div> 25 32 31 33 4 180.00 43.93200 2 ; CA- OC1- C- OC2</div></div><div><br></div><div>
I mean, if the parameters that are hiding in e.g. ...gromacs/top/amber99sb.ff could be showed in the top/itp file for human readers, that would be great.</div><div><br></div><div>Thanks,</div><div><br></div><div>Alan</div>
<div><br></div>-- <br>Alan Wilter SOUSA da SILVA, DSc<div>Bioinformatician, UniProt - PANDA, EMBL-EBI<br>CB10 1SD, Hinxton, Cambridge, UK</div><div>+44 1223 49 4588</div><br>
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