Hi Users, I constructed a .pdb file for TIP4P water model which I tried to convert to .gro using pdb2gmx using:
$ pdb2gmx -f Sim1.pdb -o Sim1.gro -water tip4p 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 =....". My .pdb file goes like this: ............ ATOM 1773 OW SOL 108 45.944 29.409 58.762 1.00 0.00 ATOM 1774 HW1 SOL 108 46.530 29.409 59.519 1.00 0.00 ATOM 1775 HW2 SOL 108 46.530 29.409 58.005 1.00 0.00 ATOM 1776 HW3 SOL 108 46.094 29.409 58.762 1.00 0.00 ............ note that the OW - HW3 is 0.15 angs as it should be. 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? Thanks, Manik Mayur Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur INDIA
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