[gmx-users] atomtype OWT4 not found but OWT3 and OWT5 is ok in amber03 force field....how is that possible?

[Kevin Channon]

Hi Mark,

  I have been experiencing a similar thing. I found that there is no
specific entry for the amber force fields in tip4p.itp file, so I
guess that gromacs was then using the default one, which has different
atom types.  For me, gromacs is in /usr/local/gromacs, so I went to
/usr/local/gromacs/share/gromacs/top, where I found tip4p.itp.  I
edited [ atoms ] section in this file from:

[ atoms ]
; id    at type res nr  residu name     at name cg nr   charge
#ifdef _FF_OPLS
1       opls_113        1       SOL      OW     1       0.0
2       opls_114        1       SOL     HW1     1       0.52
3       opls_114        1       SOL     HW2     1       0.52
4       opls_115        1       SOL      MW     1      -1.04
#else
#ifdef _FF_GROMOS96
1       OWT4            1       SOL      OW     1       0.0    15.9994
2       H               1       SOL     HW1     1       0.52    1.008
3       H               1       SOL     HW2     1       0.52    1.008
4       IW              1       SOL      MW     1      -1.04    0.0
#else
1       OWT4            1       SOL      OW     1       0.0
2       HW              1       SOL     HW1     1       0.52
3       HW              1       SOL     HW2     1       0.52
4       IW              1       SOL      MW     1      -1.04
#endif
#endif



to:



[ atoms ]
; id    at type res nr  residu name     at name cg nr   charge
#ifdef _FF_OPLS
1       opls_113        1       SOL      OW     1       0.0
2       opls_114        1       SOL     HW1     1       0.52
3       opls_114        1       SOL     HW2     1       0.52
4       opls_115        1       SOL      MW     1      -1.04
#else
#ifdef _FF_GROMOS96
1       OWT4            1       SOL      OW     1       0.0    15.9994
2       H               1       SOL     HW1     1       0.52    1.008
3       H               1       SOL     HW2     1       0.52    1.008
4       IW              1       SOL      MW     1      -1.04    0.0
#else
#ifdef _FF_AMBER99
1       amber99_61      1       SOL      OW     1       0.0   15.9994
2       amber99_60      1       SOL     HW2     1       0.52    1.008
3       amber99_60      1       SOL     HW3     1       0.52    1.008
4       MW              1       SOL     MW4     1      -1.04    0.0
#else
1       OWT4            1       SOL      OW     1       0.0
2       HW              1       SOL     HW1     1       0.52
3       HW              1       SOL     HW2     1       0.52
4       IW              1       SOL      MW     1      -1.04
#endif
#endif
#endif


i.e. added in a section that tells gromacs what to do in the case of
an amber force field.  I found this out by looking at the file
ffamber_tip4EW.itp, to see what atom types gromacs was expecting.

I hope that helps :-)

Kevin

--
Kevin Channon

School of Chemistry
University of Bristol
UK


-- 
Kevin Channon

School of Chemistry
University of Bristol
UK