use the numbers from the "BOND" section, along with measurements of the
bond lengths from the structure that concerns you.
On Mon, Sep 16, 2024 at 3:01 PM Maciej Spiegel <maciej.spiegel.umw.edu.pl>
wrote:
> The generated .frcmod is as follows:
>
> ******************
> Remark line goes here
> MASS
> os 16.000 0.465
> ca 12.010 0.360
> c2 12.010 0.360
> o 16.000 0.434
> oh 16.000 0.465
> ho 1.008 0.135
> ha 1.008 0.135
>
> BOND
> ca-os 357.50 1.370
> c2-os 371.30 1.360
> ca-ca 378.60 1.398
> c2-ca 398.40 1.385
> c2-o 635.20 1.225
> c2-c2 481.80 1.334
> c2-oh 402.30 1.339
> ho-oh 563.50 0.973
> ca-ha 395.70 1.086
> ca-o 606.50 1.236
> ca-oh 365.60 1.364
>
> ANGLE
> ca-ca-os 87.300 119.200
> c2-c2-os 88.700 121.870
> ca-c2-os 88.000 122.800 same as ce-c2-os, penalty score= 2.2
> c2-os-ca 67.800 118.200
> c2-ca-ca 68.900 120.600
> ca-ca-ca 68.800 120.020
> ca-ca-ha 48.700 119.880
> ca-c2-o 91.400 123.590 same as cc-c2-o , penalty score= 2.0
> c2-c2-ca 71.600 117.000
> c2-c2-oh 89.300 122.170
> c2-c2-c2 71.500 121.810
> c2-c2-o 89.800 130.890
> c2-oh-ho 51.800 107.630
> ca-ca-o 89.500 123.260
> ca-ca-oh 87.200 119.900
> ca-oh-ho 50.700 108.580
>
> DIHE
> c2-ca-ca-os 4 14.500 180.000 2.000
> ca-ca-ca-os 4 14.500 180.000 2.000
> ha-ca-ca-os 4 14.500 180.000 2.000
> os-c2-ca-ca 4 2.800 180.000 2.000
> c2-c2-os-ca 2 2.100 180.000 2.000
> ca-c2-os-ca 2 2.100 180.000 2.000
> o -c2-ca-ca 4 2.800 180.000 2.000
> c2-c2-ca-ca 4 2.800 180.000 2.000
> ca-ca-ca-ca 4 14.500 180.000 2.000
> ca-ca-ca-ha 4 14.500 180.000 2.000
> ca-c2-c2-oh 4 26.600 180.000 2.000
> c2-c2-c2-ca 4 26.600 180.000 2.000
> c2-ca-ca-ca 4 14.500 180.000 2.000
> c2-ca-ca-ha 4 14.500 180.000 2.000
> c2-c2-oh-ho 1 1.120 180.000 2.000
> c2-c2-c2-os 4 26.600 180.000 2.000
> o -c2-c2-oh 4 26.600 180.000 2.000
> c2-c2-c2-o 4 26.600 180.000 2.000
> oh-c2-c2-os 4 26.600 180.000 2.000
> ca-ca-ca-o 4 14.500 180.000 2.000
> ha-ca-ca-o 4 14.500 180.000 2.000
> ha-ca-ca-ha 4 14.500 180.000 2.000
> ca-ca-os-c2 2 1.800 180.000 2.000
> ca-ca-ca-oh 4 14.500 180.000 2.000
> ca-ca-oh-ho 1 0.835 180.000 2.000
> ha-ca-ca-oh 4 14.500 180.000 2.000
> o -ca-ca-oh 4 14.500 180.000 2.000
>
> IMPROPER
> ca-ca-ca-os 1.1 180.0 2.0 Using the
> default value
> c2-ca-ca-ca 1.1 180.0 2.0
> c2-ca-c2-o 1.1 180.0 2.0 Using the
> default value
> c2-c2-c2-oh 1.1 180.0 2.0 Using the
> default value
> ca-ca-ca-ha 1.1 180.0 2.0 Using general
> improper torsional angle X- X-ca-ha, penalty score= 6.0)
> ca-ca-ca-o 1.1 180.0 2.0 Using the
> default value
> c2-ca-c2-os 1.1 180.0 2.0 Using the
> default value
> ca-ca-ca-oh 1.1 180.0 2.0 Using the
> default value
>
> NONBON
> os 1.7713 0.0726
> ca 1.8606 0.0988
> c2 1.8606 0.0988
> o 1.7107 0.1463
> oh 1.8200 0.0930
> ho 0.3019 0.0047
> ha 1.4735 0.0161
> ******************
>
>
> –
> Maciej Spiegel, MPharm PhD
> *assistant professor*
> .GitHub <https://farmaceut.github.io>
>
> *Department of Organic Chemistry **and **Pharmaceutical Technology,*
> *Faculty of Pharmacy, **Wroclaw Medical University*
> *Borowska 211A, **50-556 Wroclaw, Poland*
>
> Wiadomość napisana przez Carlos Simmerling <carlos.simmerling.gmail.com>
> w dniu 16.09.2024, o godz. 20:49:
>
> it's hard to tell from a picture, you might want to measure the bond
> lengths and compare to those in the frcmod file.
>
> On Mon, Sep 16, 2024 at 2:35 PM Maciej Spiegel via AMBER <
> amber.ambermd.org> wrote:
>
>> Hello,
>>
>> I found a tutorial and followed it to parametrise the ligand below:
>>
>> https://i.sstatic.net/6HyFgwEB.png
>>
>> To say, the following commands were utilised consecutively:
>>
>> ************
>> antechamber -i LIG.mol2 -fi mol2 -o LIG.gjf -fo gcrt -gv 1 -ge LIG.gesp
>> -pf y -nc -2 -at gaff2
>> g16 LIG.gjf
>> antechamber -i LIG.gesp -fi gesp -o LIG_resp.ac -fo ac -c resp -at
>> gaff2 -rn LIG -pf y
>> antechamber -i LIG_resp.ac -fi ac -c wc -cf LIG.crg
>> espgen -i LIG.gesp -o LIG.esp
>> respgen -i LIG_resp.ac -o LIG.respin1 -f resp1
>> respgen -i LIG_resp.ac -o LIG.respin2 -f resp2
>> resp -O -i LIG.respin1 -o LIG.respout1 -p LIG.pch1 -q LIG_mod.crg -t
>> LIG.chg1 -e LIG.esp
>> resp -O -i LIG.respin2 -o LIG.respout2 -p LIG.pch2 -q LIG.chg1 -t
>> LIG.chg2 -e LIG.esp
>> cp LIG_resp.ac LIG_resp_final.ac
>> prepgen -i LIG_resp_final.ac -o LIG.prepc -f car -rn LIG
>> parmchk2 -i LIG.prepc -o LIG.frcmod -f prepc -p
>> $AMBERHOME/dat/leap/parm/gaff2.dat -pf 1 -a Y
>> ************
>>
>> Then using tLeap:
>>
>> ************
>> source leaprc.gaff2
>> source leaprc.protein.ff19SB
>> source leaprc.water.tip3p
>> source leaprc.lipid21
>> loadamberparams frcmod.ionsjc_tip3p
>> loadamberprep LIG.prepc
>> loadamberparams LIG.frcmod
>> prot = loadpdb MD.pdb
>> charge prot
>> addions2 prot Cl- 3
>> solvateoct prot TIP3PBOX 12.0
>> saveamberparm prot MD.prmtop MD.inpcrd
>> ************
>>
>> Everything went fine. However, once the molecular dynamics started, I
>> noticed that the bonds appear *off*, e.g., the C-O-C bonds seem elongated.
>>
>>
>> https://i.sstatic.net/FGLRu3Vo.png
>>
>> I am not very keen with MD and henceforth don't know where might be the
>> issue. The `atomtypes` seem reasonable:
>>
>> https://i.sstatic.net/vfRt5Co7.png
>>
>> Thanks in advance!
>> –
>> Maciej Spiegel, MPharm PhD
>> assistant professor
>> .GitHub <https://farmaceut.github.io/>
>>
>> Department of Organic Chemistry and Pharmaceutical Technology,
>> Faculty of Pharmacy, Wroclaw Medical University
>> Borowska 211A, 50-556 Wroclaw, Poland
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Mon Sep 16 2024 - 12:30:02 PDT
