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
>
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>
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Received on Mon Sep 16 2024 - 12:00:02 PDT
