Yu,
Do I understand correctly that you are now asking why you get a file
named system.${water_ff}.pdb
instead of system.opc.pdb when you run this?
Cheers,
Todd
On Fri, Jan 26, 2024 at 4:37 PM Yu Chen <yuc94.zedat.fu-berlin.de> wrote:
> Dear Todd,
>
> I greatly appreciate your prompt response. Attached below is the content
> of the bash script. I would be grateful if you could review it and identify
> any potential reason that I got the output file ’system.${water_ff}.pdb’
> with renumbering residues.
>
> #!/bin/bash
>
>
> ################################## Receptor
> ######################################
>
> rcp_nm=8EFO_protein # the file name of ligand without suffix `pdb`
>
> rcp_ff=leaprc.protein.ff19SB
>
>
>
> ## Clean the PDB file by pdb4amber
>
> pdb4amber -i ${rcp_nm}.pdb -o ${rcp_nm}_amber.pdb
>
>
> ## `tleap` requires that all residues and atoms have appropriate types to
> ensure compatibility with the specified force field.
>
> ## To avoid `tleap` failing, we delete non-essential atoms, such as
> hydrogens, but preserve important atoms like carbon and nitrogen within the
> caps residues.
>
> ## Don' worry about the missing atoms as tleap has the capability to
> reconstruct them automatically.
>
> awk '! ($2 ~ "(CH3|HH31|HH32|HH33)" || $3 ~ "(CH3|HH31|HH32|HH33)" )'
> ${rcp_nm}_amber.pdb > ${rcp_nm}_amber_f.pdb
>
> grep -v '^CONECT' ${rcp_nm}_amber_f.pdb > ${rcp_nm}_cnt_rmv.pdb
>
>
> ################################## Ligand
> ######################################
>
> # Normal Ligand
>
> nmLigFile=8QY # the file name of ligand without suffix `.pdb` or `.sdf`
>
> obabel ${nmLigFile}.pdb -O ${nmLigFile}.sdf -p # convert to sdf file for
> openmmdl_analysis, -p: add hydrogens appropriate for pH7.4
>
> charge_method=bcc # refers to the charge method that antechamber will adopt
>
> charge_value=1 # Enter the net molecular charge of the ligand as integer
> (e.g. 1 or -2)
>
> lig_ff=gaff2 # Ligand force field
>
>
> ## Clean the PDB file by pdb4amber
>
> pdb4amber -i ${nmLigFile}.pdb -o ${nmLigFile}_amber.pdb
>
>
> ## Generate a prepc file and an additional frcmod file by `antechamber`
>
> antechamber -fi pdb -fo prepc -i ${nmLigFile}_amber.pdb -o
> ${nmLigFile}.prepc -c ${charge_method} -at ${lig_ff} -nc ${charge_value}
> -pf y
>
> parmchk2 -f prepc -i ${nmLigFile}.prepc -o ${nmLigFile}.frcmod
>
>
> ## Rename ligand pdb
>
> antechamber -i ${nmLigFile}.prepc -fi prepc -o rename_${nmLigFile}.pdb -fo
> pdb
>
> ###################### Combine All Components to Be Modelled
> ####################
>
> cat > tleap.combine.in <<EOF
>
>
> source ${rcp_ff}
>
> source leaprc.${lig_ff}
>
>
> loadamberprep ${nmLigFile}.prepc
>
> loadamberparams ${nmLigFile}.frcmod
>
>
> rcp = loadpdb ${rcp_nm}_cnt_rmv.pdb
>
> nmLig = loadpdb rename_${nmLigFile}.pdb
>
> comp = combine{rcp nmLig}
>
> savepdb comp comp.pdb
>
>
> quit
>
>
> EOF
>
>
> tleap -s -f tleap.combine.in > tleap.combine.out
>
> grep -v '^CONECT' comp.pdb > comp_cnt_rmv.pdb
>
>
> ################################ Add Water/Membrane
> ##############################
>
> lipid_tp=POPC
>
> lipid_ratio=1
>
> lipid_ff=lipid21
>
> dist2Border=15 # The minimum distance between the maxmin values for x y
> and z to the box boundaries. Flag --dist
>
> padDist=17 # The width of the water layer over the membrane or protein in
> the z axis. Flag --dist_wat
>
> water_ff=opc
>
> pos_ion=Na+
>
> neg_ion=Cl-
>
> ionConc=0.15
>
>
>
> ## Build the membrane
>
> packmol-memgen --pdb comp.pdb --lipids ${lipid_tp} --ratio ${lipid_ratio}
> --preoriented --dist ${dist2Border} --dist_wat ${padDist} --salt --salt_c
> ${pos_ion} --saltcon ${ionConc} --nottrim --overwrite --notprotonate
>
>
> ## Clean the complex pdb by `pdb4amber` for further `tleap` process
>
> pdb4amber -i bilayer_comp.pdb -o clean_bilayer_comp.pdb
>
> grep -v '^CONECT' clean_bilayer_comp.pdb > clean_bilayer_comp_cnt_rmv.pdb
>
>
> ##################### Generate Prmtop and Frcmod File for the Complex
> ######################
>
> cat > tleap.in <<EOF
>
>
> source ${rcp_ff}
>
> source leaprc.water.${water_ff}
>
> source leaprc.${lig_ff}
>
> source leaprc.${lipid_ff}
>
>
> loadamberprep ${nmLigFile}.prepc
>
> loadamberparams ${nmLigFile}.frcmod
>
>
> system = loadpdb clean_bilayer_comp_cnt_rmv.pdb
>
>
> setBox system "vdw"
>
> check system
>
> charge system
>
>
> savepdb system system.${water_ff}.pdb
>
> saveamberparm system system.${water_ff}.prmtop system.${water_ff}.inpcrd
>
>
> quit
>
>
> EOF
>
>
> tleap -s -f tleap.in > tleap.out
> ---------------------------------------------------------
> Yu Chen (M.Sc., Frau/Ms)
>
> Ph.D Student
>
> Freie Universität Berlin
> Department of Biology, Chemisty, and Pharmacy
> Institute of Pharmacy
> Research Group Prof. Dr. Gerhard Wolber
>
> Königin-Luise-Str. 2+4 , 14195
> Room 180, Front Building
> Berlin / Germany
>
> yu.chen.fu-berlin.de
>
>
>
>
>
>
>
>
>
>
> On 26 Jan 2024, at 22:58, Todd Minehardt via AMBER <amber.ambermd.org>
> wrote:
>
> Yu,
>
> pdb4amber is part of AmberTools and produces a file (stdout_renum.txt) that
> maps original residue numbers to processed ones; how you would apply this
> is something I have never done, as I just work with the shifted portions
> and go from there with my analysuis. That being said, I'm sure it can be
> done.
>
> Also, the bash script you attached didn't make it across intact, if you can
> please resend it and/or include it in the body of the email, that would
> be helpful.
>
> Cheers,
>
> Todd
>
> On Fri, Jan 26, 2024 at 3:36 PM Yu Chen via AMBER <amber.ambermd.org>
> wrote:
>
> Dear Amber Community,
>
> I am currently utilizing AmberTools 22.0, installed via conda, to prepare
> the .prmtop, .inpcrd, and the corresponding system in PDB format for a
> GPCR-ligand complex for MD simulation. I have attached the bash script I
> use for your reference.
> 
>
> The residue numbering for GPCR adheres to the Ballesteros Weinstein
> numbering system. Therefore, it is crucial for the output system PDB file
> to maintain this numbering. However, I’ve noticed that after inputting the
> original protein PDB (where the residue number starts from, for instance,
> 66) into AmberTools, the residue numbering in the output system PDB file
> starts from 1. This discrepancy poses a challenge when identifying key
> interactions with certain reserved GPCR residues during post-MD analysis.
>
> I am seeking advice on whether there is a feature in AmberTools that can
> preserve the original residue numbering in the output PDB file.
>
> Any insights or guidance on how to address this issue would be greatly
> appreciated.
>
> Best regards,
> Yu Chen
> ---------------------------------------------------------
> Yu Chen (M.Sc., Frau/Ms)
>
> Ph.D Student
>
> Freie Universität Berlin
> Department of Biology, Chemisty, and Pharmacy
> Institute of Pharmacy
> Research Group Prof. Dr. Gerhard Wolber
>
> Königin-Luise-Str. 2+4 , 14195
> Room 180, Front Building
> Berlin / Germany
>
> yu.chen.fu-berlin.de
>
>
>
>
>
>
>
>
>
>
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Received on Fri Jan 26 2024 - 15:00:03 PST
