On 5/04/2011 9:59 PM, ahmet yıldırım wrote:
Dear Mark,
Now, are the files correct?
They're well-formed, but you've not taken Tsjerk's advice and arranged
for (COH)3(NH3+)C to have charges consistent with its symmetry. When
people donate their time to you, please use it or demonstrate why you
shouldn't :-)
Mark
*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
<mailto: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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