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