dear gromacs users,
i have the following problem:
i did md simulations of a solvated system (amber tip4p water) containg protein
and DNA using the amber ports.
analyzing the trajectory of my simulation i found ONE interesting system
confugurations which i wrote into a pdb file using the "trjconv - dump"
command.
now i want to merge the chains of this pdb file by using "pdb2gmx -merge"
command in order to apply distance restraints between the DNA and the protein
in an upcoming simulation.
therefore i changed the water nomenclature as advised on the amber ports for
gromacs url from SOL (with OW, HW2, HW3 and MW4) into T4P (with OW, HW2, HW3
and MW4). pdb2gmx works fine after adding T4P into the ffamber03.hdb.
Unfortunately grompp complains and prints the following warning for each T4P
residues (formerly SOL) to stdout:
grompp problem: ERROR 12 [file "test.pdb.top", line 97]:
atom MW4 (Res T4P-10) has mass 0
i added the following lines into the ffamber03_tip4p.itp but the error is
still there. HAs anyone an idea of how to get rid of this ?
Thank you very much in advance.
greetings
joern
[ moleculetype ]
; molname nrexcl
T4P
#ifdef _FF_AMBER03
1 amber99_63 1 T4P OW 1 0
16.00000
2 amber99_62 1 T4P HW2 1 0.52 1.00800
3 amber99_62 1 T4P HW3 1 0.52 1.00800
4 MW 1 T4P MW4 1 -1.04 0.00000
#endif
; at type res nr res name at name cg nr charge mass
[ settles ]
; i funct doh dhh
1 1 0.09572 0.15139
[ dummies3 ]
; Dummy from funct a b
4 1 2 3 1 0.128012065 0.128012065
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
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