On 31/03/2011 6:17 PM, ahmet yıldırım wrote:
Dear Tsjerk,
I will ask you one thing but please do not get angry (I know you are
not a private tutor but I need your helps).
How do I apply on the files (EDO.itp and TRS.itp) that you said? (or
can you suggest a tutorial?)
You'll need to become familiar with the file format, so that you know
what all the columns of data mean, so you know where the charge groups
are specified. Chapter 5 of the manual is your first port of call. If
you have read that and still have questions about detail, please ask on
the list :-)
Mark
2011/3/31 Mark Abraham <[email protected]
<mailto:[email protected]>>
On 31/03/2011 5:18 PM, ahmet yıldırım wrote:
Dear users,
Before energy minimization step , I performed the preprosessing
step using grompp .
However, there are two note that :
*_NOTE 1 [file topol.top, line 52]:_*
System has non-zero total charge: -1.500000e+01
This is an integer. See
http://en.wikipedia.org/wiki/Scientific_notation#E_notation and
http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
_*NOTE 2 [file topol.top]:*_
The largest charge group contains 11 atoms.
Since atoms only see each other when the centers of geometry of
the charge
groups they belong to are within the cut-off distance, too
large charge
groups can lead to serious cut-off artifacts.
For efficiency and accuracy, charge group should consist of a
few atoms.
For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2,
CO, etc.
See Tsjerk's email.
Mark
*
PS: *TRS and EDO are not aminoacid*
_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 2 0.055 12.0110
5 CH2 1 TRS C3 2 0.049 14.0270
6 OA 1 TRS O3 2 -0.205 15.9994
7 H 1 TRS H33 2 0.019 1.0080
8 NL 1 TRS N 2 0.206 14.0067
9 H 1 TRS H2 2 0.004 1.0080
10 H 1 TRS H3 2 0.004 1.0080
11 H 1 TRS H1 2 0.004 1.0080
12 CH2 1 TRS C2 2 0.050 14.0270
13 OA 1 TRS O2 2 -0.205 15.9994
14 H 1 TRS H23 2 0.019 1.0080
...
_*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 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
...
_*
topol.top:*_
..
; Include water topology
#include "gromos43a1.ff/spc.itp"
#include "TRS.itp"
#include "EDO.itp"
..
[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
SOL 185
SOL 143
TRS 1
EDO 1
SOL 44125
*_
Conf.gro:_*
MTA/SAH NUCLEOSIDASE; 5 NUCLEOSIDASE
5354
2GLN N 1 1.458 -1.158 0.739
2GLN H1 2 1.520 -1.083 0.763
.......
485HOH HW1 5333 0.221 -3.864 -2.291
485HOH HW2 5334 0.303 -3.946 -2.407
1TRS O1 1 -3.812 -0.471 -2.002
1TRS H13 2 -3.865 -0.443 -1.922
1TRS C1 3 -3.672 -0.469 -1.971
1TRS C 4 -3.635 -0.571 -1.863
1TRS C3 5 -3.711 -0.547 -1.731
1TRS O3 6 -3.694 -0.414 -1.679
1TRS H33 7 -3.746 -0.404 -1.594
1TRS N 8 -3.673 -0.705 -1.911
1TRS H2 9 -3.625 -0.725 -1.996
1TRS H3 10 -3.771 -0.707 -1.927
1TRS H1 11 -3.649 -0.774 -1.842
1TRS C2 12 -3.483 -0.573 -1.840
1TRS O2 13 -3.428 -0.445 -1.806
1TRS H23 14 -3.470 -0.412 -1.722
1EDO OAB 1 0.307 -2.792 0.149
1EDO HAE 2 0.390 -2.826 0.104
1EDO CAA 3 0.239 -2.901 0.212
1EDO CAC 4 0.111 -2.851 0.281
1EDO OAD 5 0.144 -2.763 0.388
1EDO HAF 6 0.060 -2.731 0.432
8.13100 7.04165 13.54850 0.00000 0.00000 -4.06550
0.00000 0.00000 0.00000
How can I fixed these notes(note 1 and note 2)?
Thanks in advance
--
Ahmet YILDIRIM
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--
Ahmet YILDIRIM
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