<div dir="ltr">Hello, I've searched the archives in search of an answer for my problem and was able to solve only part of the problem.<br>I am working with a DNA/Protein system with AMBER99 forcefield. <br>The first problem is <br>
"...Generated 2628 of the 2628 non-bonded parameter combinations<br>Generating 1-4 interactions: fudge = 0.5<br>Generated 2628 of the 2628 1-4 parameter combinations<br>ERROR 0 [file "1VKX_C.itp", line 420]:<br>
No default Bond types<br>ERROR 0 [file "1VKX_C.itp", line 1803]:<br> No default Angle types<br>ERROR 0 [file "1VKX_C.itp", line 1805]:<br> No default Angle types<br>ERROR 0 [file "1VKX_D.itp", line 418]:<br>
No default Bond types<br>ERROR 0 [file "1VKX_D.itp", line 1782]:<br> No default Angle types<br>ERROR 0 [file "1VKX_D.itp", line 1784]:<br> No default Angle types<br>Excluding 3 bonded neighbours for Protein_A 1<br>
Excluding 3 bonded neighbours for Protein_B 1<br>Excluding 3 bonded neighbours for Protein_C 1<br>Excluding 3 bonded neighbours for Protein_D 1<br>Excluding 2 bonded neighbours for SOL 23807<br>
NOTE:<br> System has non-zero total charge: -1.214508e+02<br><br>processing coordinates...<br>double-checking input for internal consistency...<br>renumbering atomtypes...<br>converting bonded parameters...<br># BONDS: 9500<br>
# ANGLES: 16856<br># PDIHS: 1881<br># RBDIHS: 19280<br># LJ14: 23897<br># SETTLE: 23807<br><br>-------------------------------------------------------<br>Program grompp, VERSION 3.3.3<br>Source code file: grompp.c, line: 1205<br>
<br>Fatal error:<br>There were 6 errors in input file(s)<br>-------------------------------------------------------..."<br>And the second error is the total system carge which is a non integral charge.<br>I've looked for the " ERROR 0 [file "1VKX_C.itp", line 420]:<br>
No default Bond types" solution but no one seams to have had the same problem as I.<br>I believe the charge problem can be found in the users list, so the actual doubt lies in the first problem.<br>Thank you in advance<br>
Fabrício Bracht<br><br></div>