GROMACS用GBSA不支援鋅離子

用GROMACS-5.1.2，想要用GBSA（Generalized Born model augmented with the hydrophobic solvent accessible surface area (SA) term）這種implicit water來跑含有zinc ion的系統，結果出現下面的錯誤訊息：

Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 18 atomtypes or they might be negative.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

應該是因為沒有鋅離子相關的參數

用下面的指令去找
$ cd /pkg/gromacs-5.1.2/share/gromacs/top
$ find . -name "*gb*" 
./amber03.ff/gbsa.itp
./oplsaa.ff/gbsa.itp
./amber96.ff/gbsa.itp
./amber99.ff/gbsa.itp
./amber99sb-ildn.ff/gbsa.itp
./amber94.ff/gbsa.itp
./charmm27.ff/gb.itp
./amber99sb.ff/gbsa.itp
./amberGS.ff/gbsa.itp

這邊看到有支援GBSA的force fields只有OPLS/AA、AMBER系列、CHARMM 27，但是沒有GROMOS。再用下面的指令來看哪些有支援zinc，發現沒有任何一種有支援：

$ grep -i 'ZN' `find ./ -name "gb*.itp" -print`

另外測試看哪些支援sodium：
$ grep -i 'NA' `find ./ -name "gb*.itp" -print`
./amber03.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./oplsaa.ff/gbsa.itp:opls_283   0.18   1     1.276    0.190    0.72 ; CA on C-terminal ALA,CYS,SER,THR,HIS,ASP,ASN
./oplsaa.ff/gbsa.itp:opls_284   0.19   1     1.045    0.190    0.72 ; CA on C-terminal GLY
./oplsaa.ff/gbsa.itp:opls_285   0.18   1     1.276    0.190    0.72 ; CA on C-terminal PRO
./oplsaa.ff/gbsa.itp:opls_309   0.16   1     1.215    0.1625   0.79 ; N (R2NH2+), N-terminal PRO NH2+
./amber96.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./amber99.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./amber99sb-ildn.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./amber94.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./amber99sb.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N
./amberGS.ff/gbsa.itp:NA           0.155    1      1.028    0.155   0.79 ; N

由此可知要用GROMACS跑implicit water的分子模擬的時候，很有可能沒辦法跑

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