Dear Mark,
Now, are the files correct?
*EDO.itp*:
[ moleculetype ]
; Name nrexcl
EDO 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 EDO OAB 1 -0.111 15.9994
2 H 1 EDO HAE 1 0.031 1.0080
3 CH2 1 EDO CAA 1 0.080 14.0270
4 CH2 1 EDO CAC *2* 0.080 14.0270
5 OA 1 EDO OAD *2* -0.111 15.9994
6 H 1 EDO HAF *2 * 0.031 1.0080
*TRS.itp:*
[ moleculetype ]
; Name nrexcl
TRS 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 OA 1 TRS O1 1 -0.119 15.9994
2 H 1 TRS H13 1 0.032 1.0080
3 CH2 1 TRS C1 1 0.087 14.0270
4 CCl4 1 TRS C *3* 0.055 12.0110
5 CH2 1 TRS C3 * 4 * 0.049 14.0270
6 OA 1 TRS O3 *4* -0.205 15.9994
7 H 1 TRS H33 * 4* 0.019 1.0080
8 NL 1 TRS N * 5* 0.206 14.0067
9 H 1 TRS H2 * 5* 0.004 1.0080
10 H 1 TRS H3 *5* 0.004 1.0080
11 H 1 TRS H1 *5 * 0.004 1.0080
12 CH2 1 TRS C2 *6 * 0.150 14.0270
13 OA 1 TRS O2 *6* -0.205 15.9994
14 H 1 TRS H23 * 6* 0.019 1.0080
Thanks for your helps
05 Nisan 2011 09:03 tarihinde Mark Abraham <mark.abra...@anu.edu.au> yazdı:
> On 5/04/2011 3:57 PM, ahmet yıldırım wrote:
>
> Dear Tsjerk,
>
> Hi Ahmet,
>>
>> As suggested, it's better to break up your molecule into smaller
>> charge groups. Note that charge groups don't need to have zero charge,
>> nor integer charge. In your case, I'd suggest two COH groups for EDO,
>> which will have zero net charge each, and for TRS I'd take the COH
>> groups as separate charge groups. I also note that the COH groups,
>> although chemically identical - H3NC(COH)3, right?-, have different
>> charges. That doesn't seem proper.
>>
>> Hope it helps,
>>
>> Tsjerk
>>
>
> nonrevised .itp file:
> EDO 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 EDO OAB 1 -0.111 15.9994
> 2 H 1 EDO HAE 1 0.031 1.0080
> 3 CH2 1 EDO CAA 1 0.080 14.0270
> 4 CH2 1 EDO CAC 1 0.080 14.0270
> 5 OA 1 EDO OAD 1 -0.111 15.9994
> 6 H 1 EDO HAF 1 0.031 1.0080
>
> nonrevised .itp file:
> EDO 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 OA 1 EDO OAB 1 -0.111 15.9994
> 2 H 1 EDO HAE 1 0.031 1.0080
> 3 CH2 1 EDO CAA 1 *0.000* 14.0270
> 4 CH2 1 EDO CAC 1 *0.000* 14.0270
> 5 OA 1 EDO OAD 1 -0.111 15.9994
> 6 H 1 EDO HAF 1 0.031 1.0080
>
> can you show me on the itp file? how do I seperate two COH groups? Please
> help me
>
>
> We didn't say to use zero *charges*. We said you need small charge groups.
> Since EDO is neutral, then by symmetry each half must also be neutral.
>
> Have a look at the way charge groups are used in the .rtp file for your
> forcefield. You need to do similar things. If you don't understand the file
> formats yet, you need to read up on chapter 5 of the manual.
>
> Mark
>
> --
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--
Ahmet YILDIRIM
--
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