<div dir="ltr">Hello,<br><br>I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here is my code for the aminoacids.c.tdb <br>
<br>[ COO- ]<br><br>[ replace ]<br>H H 1.00800 0.27190<br>N N 14.01000 -0.41570<br>CA CT 12.01000 0.03370<br>HA H1 1.00800 0.08230<br>C C 12.01000 0.59730<br>CB CT 12.01 -0.1825<br>
HB1 HC 1.008 0.0603<br>HB2 HC 1.008 0.0603<br>HB3 HC 1.008 0.0603<br> <br>[ add ]<br>1 1 O C CA N<br> O 16.00000 -0.56790<br> <br>[ bonds ]<br>C O 1 0.12290 476976.0<br>
<br>[ delete ]<br>OC1<br>OC2<br><br><br>when I run pdb2gmx using this termini modification, everything works fine except the deletion of OC1 and OC2 atoms, the error which I get for this run as follows,<br><br>Fatal error:<br>
Atom OC2 not found in residue <a href="http://seq.nr">seq.nr</a>. 8 while adding atom<br><br><br>any suggestion to delete the OC1 and OC2 atoms. If I dont enable this [ delete ] option with the aminoacids.c.tdb file, it works fine by adding the O atom to the terminal residue including the presence of OC1 and OC2 atoms. first I am trying to modify the c terminal residue. <br>
<br>Regards,<br>vijay. <br></div>