[gmx-users] virtusal site setting

[라지브간디]

Dear Richard,


For instance, To simulate the hemoglobin with heme ligated CO, would like to set the charges on center of mass of CO. 


How do i include the virtual sites atom in co-ordinates (x,y and z)?. I added the virtual sites line in topology as follows:


[ moleculetype ]
; molname       nrexcl
CMO             2


[ atoms ]
; id    at type res nr  residu name     at name cg nr   charge
1       OM              1       CMO     O     1      -0.85    15.9994
2       CM              1       CMO     C     1      -0.75    12.0110
3       COM            1       CMO     M    1        1.60     0.000


[ bonds ]
; i     j       funct   length  force.c.
1       2       1      0.1128  933032.0


[ virtual_sites2 ]
; Vsite from                  funct   a               
3       1       2               1       0.042880515






Also, i entered in .atp and .rtp file. Could you please give some procedure to do this? Thanks in advance.




Dear Rajiv, 

Without a clear explanation of what you are doing and the specific error 
message from grompp it is impossible to offer any sensible advice. 

Other pieces of information which might be useful would be, the topology 
file, the actual grompp line, and the gro file for a single CO molecule 

Richard 

On 28/03/2013 20:02, "����������" <rajiv at kaist.ac.kr> wrote: 

>Dear gmx, 
> 
>I would like to set virtual sites for CO molecules with some specific 
>charge. 
> 
>As per GROMACS manual, I've created virtual site2 in topology file for 
>CO. Also, given the information in .rtp file as well as added the 
>COM(center of mass) atom in .gro file. However, when I use gromp, it 
>shows COM not found. 
> 
>Please need an advice. Thanks. 
> 
>Rajiv