[AMBER] How to generate parameter files of N-terminal modified amino acid residue?

From: Shankha Banerjee <shankhabanerjee2012.gmail.com>
Date: Thu, 12 Sep 2019 13:26:30 +0530

 Dear Amber Users
I am trying to simulate a protein (37 aa residues) where the first residue
(ASP) is bonded with a myristic acid. Since this makes the ASP residue a
modified one, I tried following the steps mentioned in the tutorial B5 of
Amber (http://ambermd.org/tutorials/basic/tutorial5/). I was stuck at the
step where I had to make a .mc file to generate .prepin file.

In that process, I added an extra oxygen atom (name O and atom number 56 in
PDB file) to the C terminal 'C' atom of the modified AA residue to complete
its
structure. I mentioned total charge as -2 (one unit of negative charge for
side-chain carboxylate and one unit for C-terminal carboxylate) and
generated .ac file using antechamber. As the modified AA residue is at C
terminal end, while I wrote .mc file, I mentioned only TAIL_NAME,
MAIN_CHAIN, OMIT_NAME, POST_TAIL_NAME and
CHARGE. Here in .mc file, I gave CHARGE -1, as there will be only
side-chain carboxylate group, once this modified AA residue is connected to
a polypeptide chain.

Please find the PDB file (
*5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.pdb*), .ac file (
*5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.ac*) and .mc file (
*5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.mc*), what I have used for
this modified AA residue, in attachment. Here is the error came when I
called prepgen as given in tutorial B5.

COMMAND USED- prepgen -i
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.ac -o
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.prepin -m
5md_myr_fromVMD_AM1_3_trunketedMYR_ASP_O_added.mc

ERROR MESSAGE-
POST_TAIL_TYPE is N
Net charge of truncated molecule is -1.00
TAIL_ATOM 53 C14
MAIN_CHAIN 1 45 CA
MAIN_CHAIN 2 43 N
MAIN_CHAIN 3 1 C
MAIN_CHAIN 4 3 C1
MAIN_CHAIN 5 4 C2
MAIN_CHAIN 6 7 C3
MAIN_CHAIN 7 10 C4
MAIN_CHAIN 8 15 C5
MAIN_CHAIN 9 16 C6
MAIN_CHAIN 10 19 C7
MAIN_CHAIN 11 24 C8
MAIN_CHAIN 12 25 C9
MAIN_CHAIN 13 28 C10
MAIN_CHAIN 14 31 C11
MAIN_CHAIN 15 36 C12
MAIN_CHAIN 16 37 C13
MAIN_CHAIN 17 53 C14
OMIT_ATOM 1 55 O2
Number of mainchain atoms (including head and tail atom): 17
/home/dynamix/sware/amber16/amber16/bin/prepgen: line 4: 26739
Segmentation fault (core dumped)
$AMBERHOME/bin/to_be_dispatched/prepgen "$."


Then I tried another method following suggestions from the community where
I took the whole peptide along with myristic acid and called protein amber
protein force field for the polypeptide unit and lipid17 force field for
myristic acid unit. I used the following input file:


source leaprc.protein.ff14SB
source leaprc.lipid17
#source leaprc.gaff
RM = loadpdb myr-pro-1.pdb
savepdb RM myr-pro-1_out.pdb
saveAmberParm RM myr-pro-1.top myr-pro-1.crd
quit

But the parameter files failed to generate. The leap log file is as follows:

log started: Thu Sep 12 12:27:04 2019

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff14SB force field
>> # ----- NOTE: this is designed for PDB format 3!
>> #
>> # load atom type hybridizations
>> #
>> addAtomTypes {
>> { "H" "H" "sp3" }
>> { "HO" "H" "sp3" }
>> { "HS" "H" "sp3" }
>> { "H1" "H" "sp3" }
>> { "H2" "H" "sp3" }
>> { "H3" "H" "sp3" }
>> { "H4" "H" "sp3" }
>> { "H5" "H" "sp3" }
>> { "HW" "H" "sp3" }
>> { "HC" "H" "sp3" }
>> { "HA" "H" "sp3" }
>> { "HP" "H" "sp3" }
>> { "HZ" "H" "sp3" }
>> { "OH" "O" "sp3" }
>> { "OS" "O" "sp3" }
>> { "O" "O" "sp2" }
>> { "O2" "O" "sp2" }
>> { "OP" "O" "sp2" }
>> { "OW" "O" "sp3" }
>> { "CT" "C" "sp3" }
>> { "CX" "C" "sp3" }
>> { "C8" "C" "sp3" }
>> { "2C" "C" "sp3" }
>> { "3C" "C" "sp3" }
>> { "CH" "C" "sp3" }
>> { "CS" "C" "sp2" }
>> { "C" "C" "sp2" }
>> { "CO" "C" "sp2" }
>> { "C*" "C" "sp2" }
>> { "CA" "C" "sp2" }
>> { "CB" "C" "sp2" }
>> { "CC" "C" "sp2" }
>> { "CN" "C" "sp2" }
>> { "CM" "C" "sp2" }
>> { "CK" "C" "sp2" }
>> { "CQ" "C" "sp2" }
>> { "CD" "C" "sp2" }
>> { "C5" "C" "sp2" }
>> { "C4" "C" "sp2" }
>> { "CP" "C" "sp2" }
>> { "CI" "C" "sp3" }
>> { "CJ" "C" "sp2" }
>> { "CW" "C" "sp2" }
>> { "CV" "C" "sp2" }
>> { "CR" "C" "sp2" }
>> { "CA" "C" "sp2" }
>> { "CY" "C" "sp2" }
>> { "C0" "Ca" "sp3" }
>> { "MG" "Mg" "sp3" }
>> { "N" "N" "sp2" }
>> { "NA" "N" "sp2" }
>> { "N2" "N" "sp2" }
>> { "N*" "N" "sp2" }
>> { "NP" "N" "sp2" }
>> { "NQ" "N" "sp2" }
>> { "NB" "N" "sp2" }
>> { "NC" "N" "sp2" }
>> { "NT" "N" "sp3" }
>> { "NY" "N" "sp2" }
>> { "N3" "N" "sp3" }
>> { "S" "S" "sp3" }
>> { "SH" "S" "sp3" }
>> { "P" "P" "sp3" }
>> { "LP" "" "sp3" }
>> { "EP" "" "sp3" }
>> { "F" "F" "sp3" }
>> { "Cl" "Cl" "sp3" }
>> { "Br" "Br" "sp3" }
>> { "I" "I" "sp3" }
>> }
>> #
>> # Load the main parameter set.
>> #
>> parm10 = loadamberparams parm10.dat
Loading parameters: /home/suchetana/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod14SB = loadamberparams frcmod.ff14SB
Loading parameters: /home/suchetana/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
>> #
>> # Load main chain and terminating amino acid libraries
>> #
>> loadOff amino12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/amino12.lib
Loading: ALA
Loading: ARG
Loading: ASH
Loading: ASN
Loading: ASP
Loading: CYM
Loading: CYS
Loading: CYX
Loading: GLH
Loading: GLN
Loading: GLU
Loading: GLY
Loading: HID
Loading: HIE
Loading: HIP
Loading: HYP
Loading: ILE
Loading: LEU
Loading: LYN
Loading: LYS
Loading: MET
Loading: PHE
Loading: PRO
Loading: SER
Loading: THR
Loading: TRP
Loading: TYR
Loading: VAL
>> loadOff aminoct12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminoct12.lib
Loading: CALA
Loading: CARG
Loading: CASN
Loading: CASP
Loading: CCYS
Loading: CCYX
Loading: CGLN
Loading: CGLU
Loading: CGLY
Loading: CHID
Loading: CHIE
Loading: CHIP
Loading: CHYP
Loading: CILE
Loading: CLEU
Loading: CLYS
Loading: CMET
Loading: CPHE
Loading: CPRO
Loading: CSER
Loading: CTHR
Loading: CTRP
Loading: CTYR
Loading: CVAL
Loading: NHE
Loading: NME
>> loadOff aminont12.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/aminont12.lib
Loading: ACE
Loading: NALA
Loading: NARG
Loading: NASN
Loading: NASP
Loading: NCYS
Loading: NCYX
Loading: NGLN
Loading: NGLU
Loading: NGLY
Loading: NHID
Loading: NHIE
Loading: NHIP
Loading: NILE
Loading: NLEU
Loading: NLYS
Loading: NMET
Loading: NPHE
Loading: NPRO
Loading: NSER
Loading: NTHR
Loading: NTRP
Loading: NTYR
Loading: NVAL
>>
>> #
>> # Define the PDB name map for the amino acids
>> #
>> addPdbResMap {
>> { 0 "HYP" "HYP" } { 1 "HYP" "CHYP" }
>> { 0 "ALA" "NALA" } { 1 "ALA" "CALA" }
>> { 0 "ARG" "NARG" } { 1 "ARG" "CARG" }
>> { 0 "ASN" "NASN" } { 1 "ASN" "CASN" }
>> { 0 "ASP" "NASP" } { 1 "ASP" "CASP" }
>> { 0 "CYS" "NCYS" } { 1 "CYS" "CCYS" }
>> { 0 "CYX" "NCYX" } { 1 "CYX" "CCYX" }
>> { 0 "GLN" "NGLN" } { 1 "GLN" "CGLN" }
>> { 0 "GLU" "NGLU" } { 1 "GLU" "CGLU" }
>> { 0 "GLY" "NGLY" } { 1 "GLY" "CGLY" }
>> { 0 "HID" "NHID" } { 1 "HID" "CHID" }
>> { 0 "HIE" "NHIE" } { 1 "HIE" "CHIE" }
>> { 0 "HIP" "NHIP" } { 1 "HIP" "CHIP" }
>> { 0 "ILE" "NILE" } { 1 "ILE" "CILE" }
>> { 0 "LEU" "NLEU" } { 1 "LEU" "CLEU" }
>> { 0 "LYS" "NLYS" } { 1 "LYS" "CLYS" }
>> { 0 "MET" "NMET" } { 1 "MET" "CMET" }
>> { 0 "PHE" "NPHE" } { 1 "PHE" "CPHE" }
>> { 0 "PRO" "NPRO" } { 1 "PRO" "CPRO" }
>> { 0 "SER" "NSER" } { 1 "SER" "CSER" }
>> { 0 "THR" "NTHR" } { 1 "THR" "CTHR" }
>> { 0 "TRP" "NTRP" } { 1 "TRP" "CTRP" }
>> { 0 "TYR" "NTYR" } { 1 "TYR" "CTYR" }
>> { 0 "VAL" "NVAL" } { 1 "VAL" "CVAL" }
>> { 0 "HIS" "NHIS" } { 1 "HIS" "CHIS" }
>> }
>>
>> #
>> # assume that most often proteins use HIE
>> #
>> NHIS = NHIE
>> HIS = HIE
>> CHIS = CHIE
>
> source leaprc.lipid17
----- Source: /home/suchetana/amber18/dat/leap/cmd/leaprc.lipid17
----- Source of /home/suchetana/amber18/dat/leap/cmd/leaprc.lipid17 done
>> #
>> # Set log file
>> #
>> logFile leap.log
log started: Thu Sep 12 12:27:04 2019

Log file: ./leap.log
>> #
>> # leaprc for loading the Lipid17 v1.1 force field
>> #
>> # Load atom type hybridizations
>> #
>> addAtomTypes {
>> { "cA" "C" "sp3" }
>> { "cB" "C" "sp2" }
>> { "cC" "C" "sp2" }
>> { "cD" "C" "sp3" }
>> { "cP" "C" "sp3" }
>> { "cR" "C" "sp3" }
>> { "hA" "H" "sp3" }
>> { "hB" "H" "sp3" }
>> { "hE" "H" "sp3" }
>> { "hL" "H" "sp3" }
>> { "hN" "H" "sp3" }
>> { "hO" "H" "sp3" }
>> { "hR" "H" "sp3" }
>> { "hS" "H" "sp3" }
>> { "hX" "H" "sp3" }
>> { "nA" "N" "sp3" }
>> { "nN" "N" "sp2" }
>> { "oC" "O" "sp2" }
>> { "oH" "O" "sp3" }
>> { "oO" "O" "sp2" }
>> { "oP" "O" "sp2" }
>> { "oR" "O" "sp3" }
>> { "oS" "O" "sp3" }
>> { "oT" "O" "sp3" }
>> { "pA" "P" "sp3" }
>> }
>> #
>> # Load the Lipid17 parameter set.
>> #
>> lipid17 = loadamberparams lipid17.dat
Loading parameters: /home/suchetana/amber18/dat/leap/parm/lipid17.dat
Reading title:
AMBER Lipid17 v1.1 Force Field, A. Skjevik, C. Dickson, B. Madej, I.R.
Gould, R.C. Walker*
>> #
>> # Load the Lipid17 master lib file.
>> #
>> loadoff lipid17.lib
Loading library: /home/suchetana/amber18/dat/leap/lib/lipid17.lib
Loading: AR
Loading: CHL
Loading: DHA
Loading: LAL
Loading: MY
Loading: OL
Loading: PA
Loading: PC
Loading: PE
Loading: PGR
Loading: PH-
Loading: PS
Loading: ST
>>
>
> #source leaprc.gaff
> RM = loadpdb myr-pro-1.pdb
Loading PDB file: ./myr-pro-1.pdb

/home/suchetana/amber18/bin/teLeap: Warning!
Name change in pdb file residue 38 ;
this residue is split into MY and ASP.

/home/suchetana/amber18/bin/teLeap: Note.
1 residues had naming warnings.
Thus, there are split residues;
residue sequence numbers will not correspond to those in the pdb.
-- residue 38: duplicate [ C] atoms (total 14)
-- residue 38: duplicate [ H] atoms (total 27)

/home/suchetana/amber18/bin/teLeap: Warning!
Atom names in each residue should be unique.
     (Same-name atoms are handled by using the first
      occurrence and by ignoring the rest.
      Frequently duplicate atom names stem from alternate
      conformations in the PDB file.)

Matching PDB residue names to LEaP variables.
Mapped residue ALA, term: Terminal/last, seq. number: 37 to: CALA.
Created a new atom named: C within residue: .R<MY 38>
Created a new atom named: O within residue: .R<MY 38>
Created a new atom named: H within residue: .R<MY 38>
  Added missing heavy atom: .R<MY 38>.A<C12 38>
  Added missing heavy atom: .R<MY 38>.A<C13 35>
  Added missing heavy atom: .R<MY 38>.A<C14 32>
  Added missing heavy atom: .R<MY 38>.A<C15 29>
  Added missing heavy atom: .R<MY 38>.A<C16 26>
  Added missing heavy atom: .R<MY 38>.A<C17 23>
  Added missing heavy atom: .R<MY 38>.A<C18 20>
  Added missing heavy atom: .R<MY 38>.A<C19 17>
  Added missing heavy atom: .R<MY 38>.A<C110 14>
  Added missing heavy atom: .R<MY 38>.A<C111 11>
  Added missing heavy atom: .R<MY 38>.A<C112 8>
  Added missing heavy atom: .R<MY 38>.A<C113 5>
  Added missing heavy atom: .R<MY 38>.A<C114 2>
Created a new atom named: H3 within residue: .R<ASP 39>
  total atoms in file: 635
  Leap added 41 missing atoms according to residue templates:
       13 Heavy
       28 H / lone pairs
  The file contained 4 atoms not in residue templates
> savepdb RM myr-pro-1_out.pdb
Writing pdb file: myr-pro-1_out.pdb

/home/suchetana/amber18/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CALA -> ALA
> saveAmberParm RM myr-pro-1.top myr-pro-1.crd
Checking Unit.

/home/suchetana/amber18/bin/teLeap: Warning!
There is a bond of 14.636845 angstroms between:

/home/suchetana/amber18/bin/teLeap: Warning!
The unperturbed charge of the unit (-1.000001) is not zero.
FATAL: Atom .R<MY 38>.A<C 41> does not have a type.
FATAL: Atom .R<MY 38>.A<O 42> does not have a type.
FATAL: Atom .R<MY 38>.A<H 43> does not have a type.
FATAL: Atom .R<ASP 39>.A<H3 13> does not have a type.

/home/suchetana/amber18/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 5; Notes = 1.

In the output PDB that we get, ASP and MY got split into two residues with
a TER in between (I gave MY and ASP different residue number but still TER
was there).
I am attaching the relevant files.
Kindly help me to generate the prep and frc files for this modified residue
to simulate the structure. Since I am a beginner in this, a very detailed
and step by step instruction set with pointers to where I made mistake in
the input files would be highly appreciated.
I thank you in advance for your kind help.

*N.B.: Initially I gave 'MYR' residue name for myristic acid in the first
process but in the second process, I named myristic acid as 'MY', as in the
force field.*


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Received on Thu Sep 12 2019 - 01:00:02 PDT
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