tekle...@ualberta.ca wrote:
Dear Justin,
First of all thank you for your help..
I have developed the toplogy file for my molecule using the PRODRG
server. But the topology did not include properly the carboxylic acid
functional group ( with proton) instead the software assumes both
oxygens as identical due to resonance. Therefore I want to modify my
topology .....what do I need to do.
From the PRODRG FAQ:
"Q: PRODRG doesn't properly protonate my molecule.
A: This can be fixed by adding the command
ADDHYD atomname
or
DELHYD atomname
to your input drawing/PDB file."
No need to hack the topology. Run PRODRG once to identify which atom name it
will assign to the oxygens, then follow the instructions above.
-Justin
In side my topology (initial)
===========================================================
44 CH1 1 UNK CA 13 0.143 13.0190
45 C 1 UNK C 13 0.372 12.0110
46 OM 1 UNK OXT 13 -0.757 15.9994
47 OM 1 UNK O 13 -0.758 15.9994
============================================================
MODIFIED to the following topology
============================================================
44 CH1 1 UNK CA 13 XXX 13.0190
45 C 1 UNK C 13 XXX 12.0110
46 O 1 UNK OXT 13 XXX 15.9994
47 OA 1 UNK O 13 XXX 15.9994
48 HO 1 UNK HAA 13 XXX 1.00800
===========================================================
XXX refers to a charge of each ......
How can I allocate a charge distribution for each united atom molecule
in the modified topology .......
Remark
I checked the .RTP file and I have found the following information for the
[ ASPH] residue ....
CG C 0.53000 2
OD1 O -0.38000 2
OD2 OA -0.54800 2
HD2 HO 0.39800 2
But in this case eventhough this describes for the carboxilic acid
functional group . It does not include CH1 in the same group...... what
do I need to do to
Example
CA CH1 XXXXXXX 2
CG C 0.53000 2
OD1 O -0.38000 2
OD2 OA -0.54800 2
HD2 HO 0.39800 2
XXXXXX is the new charge for CH1 which I do not know..... can you
help..... or simply I have to put 0.00000
have a great day
Rob
***************************************************
The entire Topology is the following
; nr type resnr resid atom cgnr charge mass
1 CH3 1 UNK CAZ 1 0.000 15.0350
2 CH2 1 UNK CAK 1 0.000 14.0270
3 CH2 1 UNK CBS 2 0.000 14.0270
4 CH2 1 UNK CBL 2 0.000 14.0270
5 CH2 1 UNK CBG 3 0.000 14.0270
6 CH2 1 UNK CBM 3 0.000 14.0270
7 CH1 1 UNK CBA 3 0.000 13.0190
8 CH2 1 UNK CBD 3 0.000 14.0270
9 CH2 1 UNK CBE 3 0.000 14.0270
10 CH2 1 UNK CBF 4 0.000 14.0270
11 CH2 1 UNK CBJ 4 0.000 14.0270
12 CH2 1 UNK CBN 5 0.101 14.0270
13 CH3 1 UNK CBT 5 0.057 15.0350
14 NR6* 1 UNK NBU 5 0.069 14.0067
15 CB 1 UNK CBP 5 0.346 12.0110
16 O 1 UNK OCB 5 -0.573 15.9994
17 CB 1 UNK CAG 6 0.351 12.0110
18 O 1 UNK OCA 6 -0.565 15.9994
19 CH1 1 UNK CBI 6 0.178 13.0190
20 CR61 1 UNK CBO 6 0.018 13.0190
21 CR61 1 UNK CAV 6 0.018 13.0190
22 CB 1 UNK CAN 7 0.000 12.0110
23 CB 1 UNK CAR 7 0.000 12.0110
24 CB 1 UNK CAX 8 0.000 12.0110
25 CB 1 UNK CBC 8 0.000 12.0110
26 CR61 1 UNK CBH 8 0.000 13.0190
27 CR61 1 UNK CAW 8 0.000 13.0190
28 CH1 1 UNK CAQ 9 0.074 13.0190
29 CB 1 UNK CAM 9 0.001 12.0110
30 CR61 1 UNK CAU 9 -0.037 13.0190
31 CR61 1 UNK CAI 9 -0.038 13.0190
32 CB 1 UNK CAC 10 0.003 12.0110
33 CB 1 UNK CAE 10 0.442 12.0110
34 O 1 UNK OBX 10 -0.448 15.9994
35 CB 1 UNK CAB 10 0.003 12.0110
36 CB 1 UNK CAF 11 0.004 12.0110
37 CB 1 UNK CAJ 11 0.004 12.0110
38 CR61 1 UNK CAP 11 -0.008 13.0190
39 CR61 1 UNK CAH 12 -0.013 13.0190
40 CB 1 UNK CAA 12 0.003 12.0110
41 CB 1 UNK CAD 12 0.411 12.0110
42 O 1 UNK OBW 12 -0.483 15.9994
43 NR6* 1 UNK N 12 0.082 14.0067
44 CH1 1 UNK CA 13 0.143 13.0190
45 C 1 UNK C 13 0.372 12.0110
46 OM 1 UNK OXT 13 -0.757 15.9994
47 OM 1 UNK O 13 -0.758 15.9994
48 CH2 1 UNK CB 14 0.068 14.0270
49 CB 1 UNK CG 14 0.002 12.0110
50 CR61 1 UNK CD1 14 -0.023 13.0190
51 CR61 1 UNK CE1 14 -0.024 13.0190
52 CR61 1 UNK CZ 14 -0.023 13.0190
53 CR61 1 UNK CE2 15 0.000 13.0190
54 CR61 1 UNK CD2 15 0.000 13.0190
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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