Hi Users,<br><br>I constructed a .pdb file for TIP4P water model which I tried to convert to .gro using pdb2gmx using:<br><br>$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p<br><br>with the choice of forcefield as 5 (OPLS-AA/L all-atom force field). After conversion I found that the position of HW3(MW), the dummy atom is not the same relative to OW, what I kept in the .pdb file. Even during the conversion pdb2gmx gave warnings as "Warning: Long Bond (1773-1776 =....".<br>
My .pdb file goes like this:<br>............<br>ATOM 1773 OW SOL 108 45.944 29.409 58.762 1.00 0.00<br>ATOM 1774 HW1 SOL 108 46.530 29.409 59.519 1.00 0.00<br>ATOM 1775 HW2 SOL 108 46.530 29.409 58.005 1.00 0.00<br>
ATOM 1776 HW3 SOL 108 46.094 29.409 58.762 1.00 0.00<br>............<br>note that the OW - HW3 is 0.15 angs as it should be.<br><br>So why is pdb2gmx recalculating the co-ordinates of HW3? How is the OW-HW3 bond is getting stretched? Also, what should be the correct procedure for the conversion?<br>
<br>Thanks,<br><br clear="all">Manik Mayur<br>Graduate student<br>Microfluidics Lab<br>Dept. of Mechanical Engg.<br>IIT Kharagpur<br>INDIA<br>