[gmx-users] Topology
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 10 13:04:09 CET 2010
teklebrh at 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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