[gmx-users] Setting virtual sites ?

[Broadbent, Richard]

Please include the full error message and the grompp line you used when
asking for help. Without them I can't tell what you are doing.

Richard

On 04/04/2013 17:40, "라지브간디" <rajiv at kaist.ac.kr> wrote:

>
>Dear Richard,
>
>I've included the COM in my .gro and also updated the rtp, atp and
>ffnonbonded.itp files as well as the exact coefficient value.  But when I
>use gromp I get the error that COM not found in atom type database .
>
>Actually I included the COM in atomtypes.atp like
>COM  0.0000
>
>As it doesn't have mass value. In addition, I included in ffnonbonded.
>Itp file by setting their LJ value as 0 ( both sigma and epsilon )
>
>Please suggest how to avoid this error.
>Thanks in advance.
>
>Rajiv
>
>
>
>Dear Rajiv, 
>
>The .itp looks fine to me except for the coefficient in the virtual site
>which I think should be much closer to 0.5.
>
>If the issue is that you don't have the coordinate on the COM in your
>.gro 
>file then you will need to generate it yourself. If you have one CO
>molecule which you use to build a box usingsay genconf I would suggest
>just working out the position by hand and modifying the .gro manually. If
>that is not the case (ie. you have many CO molecules at all stages of the
>process) it's time to get out your favourite programming language and
>write a program which reads a .gro and adds the COM to each molecule and
>writes it out again.
>
>
>Richard 
>
>On 29/03/2013 06:41, "" wrote:
>>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 0.5000
>
>> 
>> 
>> 
>> 
>> 
>> 
>>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, "������������������������������" 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 
>> 
>
>
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