[gmx-users] new type atom

[David]

On Fri, 2002-12-13 at 01:22, nanyu101 wrote:
>  Hi,
>     And I hope some one can resolve my puzzle.I am looking forward to your response.
>  But there are something wrong about new type atom in my model. This model is composed of polyester, polyphosphorus and calcium.You know that calcium connects the phosphorus and four water molecules just as below:
>  [ PPI ]
>   [ atoms ]
>     OP1    OS  -0.888     1
>      P1     P   2.398     1
>     OP3    OP  -0.622     1
>     OP4    OP  -0.888     1
>     OP2    OS  -1.013     1
>      P2     P   2.398     1
>     OP5    OP  -0.888     1
>     OP6    OP  -0.888     1
>     Ca     CA   2.000     2
>    OW1     OW  -0.360     3
>    OW2     OW  -0.360     4
>    OW3     OW  -0.360     5
>    OW4     OW  -0.360     6
The charge groups should be in order, but you probably don't want to
have th ewater in there at all...

Maybe you can make a tar file with all library files and pdb file and
send it to me, I'll try to reproduce your problem then.



>    HW1     HW   0.180     3
>    HW2     HW   0.180     3
>    HW3     HW   0.180     4
>    HW4     HW   0.180     4
>    HW5     HW   0.180     5
>    HW6     HW   0.180     5
>    HW7     HW   0.180     6
>    HW8     HW   0.180     6
>  [bonds]
>    OP1    P1
>     P1   OP3
>     P1   OP4
>     P1   OP2
>    OP2    P2
>     P2   OP5
>     P2   OP6
>    OW1   HW1
>    OW1   HW2
>    OW2   HW3
>    OW2   HW4
>    OW3   HW5
>    OW3   HW6
>    OW4   HW7
>    OW4   HW8
> 
>  The atom type OP is the atom O connecting the calcium, so  I created a 
>  new atom type in ffgmx.atp file.But everytime I run pdb2gmx, the 
>  system told me that there is no OP in atp file.I have tried to copy 
>  this atp file in current direction, but it's useless.Would you please 
>  give me some advices?Thanks a lot.
> 
>  I am looking forward to your response.
> 
>  All you best,
>  Xianhui 
> 
> ______________________________________
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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