[gmx-users] Tip5p with gromos 96, error atom has mass 0

[David van der Spoel]

主月 ：） wrote:
> Hi all:
> I built a topol file for tip5p water accordint to tip5p.itp which is 
> designed for OPLS.But when i used grompp to built a tpr file, three 
> errors came even the system just have one tip5p water.
>  
> The error is :
>  
> ERROR 1 [file "topol.top", line 10]:
>   atom OW <Res SOL-1> has mass 0
> ERROR 2 [file "topol.top", line 10]:
>   atom HW1 <Res SOL-1> has mass 0
> ERROR 3 [file "topol.top", line 10]:
>   atom HW2 <Res SOL-1> has mass 0
>  
> In fact, the mass for all above atoms were all defined in atp file. How 
> can i fix it? Thanks a lot.
>  
> The build steps are follows:
> 1. Named the atom type in new tip5p.itp. Add them to ffG53a6.atp and 
> ffG53a6nb.itp.
> In tip5p.itp:
> [ atoms ]
> ; id    at type res nr  residu name     at name         cg nr   charge
> 1       5p_O     1       SOL              OW             1       0
> 2       5p_H     1       SOL             HW1             1       0.241
> 3       5p_H     1       SOL             HW2             1       0.241
> 4       5p_L     1       SOL             OL1             1      -0.241
> 5       5p_L     1       SOL             OL2             1      -0.241
> In ffG53a6.atp
>  5p_O  15.99940 ;     O TIP5P Water
>  5p_H   1.00800 ;     H TIP5P Water
>  5p_L   0.00000 ;     L TIP5P Water
> In ffG53a6nb.itp
>  5p_O    8 0.000      0.000     A  2.470013e-03  2.278383e-06
>  5p_H    1 0.000      0.000     A           0           0
>  5p_L    0 0.000      0.000     D           0           0
>  
> 2. Write top file.
> #include "ffG53a6.itp"
> #include "tip5p_.itp" 
>  
> [ system ]
> ; Name
> Protein
>  
> [ molecules ]
> ; Compound        #mols
>  SOL           1
>  
> 3. Built gro
>  
> 5
>     1SOL     OW    1   0.321   1.614   0.603
>     1SOL    HW1    2   0.377   1.643   0.675
>     1SOL    HW2    3   0.258   1.555   0.645
>     1SOL    OL1    4   0.358   1.581   0.554
>     1SOL    OL2    5   0.288   1.669   0.574
>     0.5 0.5 0.5
>  4. grompp -f em.mdp
>  
> Then the errors came.
>  
>  
> *************************************************
> Ji Qing
> Institute of Chemistry, Chinese Academy of Sciences
> Tel: 0086-10-62562894  ，82618423
> *************************************************
> 
> 
> ------------------------------------------------------------------------
> 
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put the mass in your tip5p.itp file.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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