Re: [AMBER] Non-Standard Parametrization Issue

From: He, Amy via AMBER <amber.ambermd.org>
Date: Fri, 22 Mar 2024 06:40:50 +0000

Hi Kavinda,

HEAD_NAME and TAIL_NAME are perceived as “backbone” so we don’t have to include them as MAIN_CHAIN again.

According to your description, the capping atoms are only hydrogens, so yes I think it’s correct to remove them as you did in this mc file :>

One more thing: if this residue is charged, I would specify the charge in the mc file

Get Outlook for iOS<https://aka.ms/o0ukef>
________________________________
From: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>
Sent: Friday, March 22, 2024 2:31:56 AM
To: He, Amy <he.1768.buckeyemail.osu.edu>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Non-Standard Parametrization Issue

Hi Amy, In the case of CGU, I think I have ommited the HB2 and HB3 atoms as you suggested should not be ommitted. I extracted the residue from the PDB file and checked each atom individually to see which are the ones connected to the main chain. 

Hi Amy,

In the case of CGU, I think I have ommited the HB2 and HB3 atoms as you suggested should not be ommitted. I extracted the residue from the PDB file and checked each atom individually to see which are the ones connected to the main chain. It seem to be only N, C and CA atoms. And the N atom seems to have 3 H atoms that should be removed as it is in the main chain (HN1, HN2 and HN3)? And in the C atom there is H which also should be removed? And the rest of the atoms are CB, HB2, HB3, CG, CD1, OE12, OE11, CD2, OE21 and OE22 (Which are atoms of the residue that are not connected to the main chain of osteocalcin). So in this case if I modify the main chain file is it correct as follows for CGU?

>cgu.mc
HEAD_NAME N
TAIL_NAME C
MAIN_CHAIN N
MAIN_CHAIN CA
MAIN_CHAIN C
OMIT_NAME HN1
OMIT_NAME HN2
OMIT_NAME HN3
OMIT_NAME H
PRE_HEAD_TYPE C
POST_TAIL_TYPE N
CHARGE 0.0

Thank you so much,
Kind regards,
Kavinda
________________________________
From: He, Amy <he.1768.buckeyemail.osu.edu>
Sent: Friday, March 22, 2024 11:35 AM
To: Kavinda Kashi Juliyan Gunasinghe <kkgunasinghe.swinburne.edu.my>; AMBER Mailing List <amber.ambermd.org>
Subject: Re: Non-Standard Parametrization Issue


Hi Kavinda,



The MAIN_CHAIN specification in the mainchain file might be the cause. As you described residue CGU in PDB 1Q8H is like Glu with a modified sidechain (unlike CRO in the example, CRO adds additional “backbone” atoms). In this case, we will have only exactly the alpha carbon of the nonstandard residue as MAIN_CHAIN.



Also, we probably shouldn’t omit the hydrogen atoms if they are part of the nonstandard residue (for example the hydrogens connected to beta carbon, HB2 and HB3?). What to omit depends on your input nonstandard residue model in antechamber, and OMIT_ATOM is usually used to remove the capping groups (atoms that will be gone after the residue is embedded in a protein).



Hope this helps :> 





--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Kavinda Kashi Juliyan Gunasinghe via AMBER <amber.ambermd.org>
Date: Friday, March 22, 2024 at 1:39 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Non-Standard Parametrization Issue
Hi Users,
I am having some difficulty in parameterizing 3 Gamma-carboxylated Glu (CGU) residue in the Osteocalcin protein (PDB ID: 1Q8H). I followed the GFP tutorial and followed the exact same steps for the CGU residues. However, some of the bond and angle parameters are still missing. I will provide by main chain file (cgu.mc) and the leap.log. I'm wondering why these parameters are not being found in both GAFF and ff19SB and ff14SB force fields. Is it because of an issue with my main chain file or something else? I am confused in this case as the modified residue in the GFP tutorial seem to correctly parameterize.
>cgu.mc
 PRE_HEAD_TYPE is     C
POST_TAIL_TYPE is     N
Net charge of truncated molecule is     0.00
HEAD_ATOM      1    N
TAIL_ATOM      3    C
MAIN_CHAIN     1    1    N
MAIN_CHAIN     2    1    N
MAIN_CHAIN     3    2   CA
MAIN_CHAIN     4    3    C
MAIN_CHAIN     5    4    O
OMIT_ATOM      1   15   H
OMIT_ATOM      2   16  HA
OMIT_ATOM      3    5  OXT
OMIT_ATOM      4   17  HXT
OMIT_ATOM      5   18  HB2
OMIT_ATOM      6   19  HB3
OMIT_ATOM      7   20   HG
OMIT_ATOM      8   21  HE12
OMIT_ATOM      9   22  HE22
>leap.log
started: Sat Mar  9 15:17:04 2024
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the ff19SB 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" }
>>    { "XC"  "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.
>> #
>> set default cmap on
>> parm19 = loadamberparams parm19.dat
Loading parameters: /home/juliyan/Desktop/amber20_src/dat/leap/parm/parm19.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA + ff19SB
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: EP)
>> frcmod19SB = loadamberparams frcmod.ff19SB
Loading parameters: /home/juliyan/Desktop/amber20_src/dat/leap/parm/frcmod.ff19SB
Reading force field modification type file (frcmod)
Reading title:
ff19SB AA-specific backbone CMAPs for protein 07/25/2019
>> #
>> #  Load main chain and terminating amino acid libraries
>> #
>> loadOff amino19.lib
Loading library: /home/juliyan/Desktop/amber20_src/dat/leap/lib/amino19.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/juliyan/Desktop/amber20_src/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/juliyan/Desktop/amber20_src/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" "NHYP" } { 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.gaff
----- Source: /home/juliyan/Desktop/amber20_src/dat/leap/cmd/leaprc.gaff
----- Source of /home/juliyan/Desktop/amber20_src/dat/leap/cmd/leaprc.gaff done
>> logFile leap.log
log started: Sat Mar  9 15:17:11 2024
Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> #       This file is mostly for use with Antechamber
>> #
>> #  load atom type hybridizations
>> #
>> addAtomTypes {
>>    { "h1"  "H" "sp3" }
>>    { "h2"  "H" "sp3" }
>>    { "h3"  "H" "sp3" }
>>    { "h4"  "H" "sp3" }
>>    { "h5"  "H" "sp3" }
>>    { "ha"  "H" "sp3" }
>>    { "hc"  "H" "sp3" }
>>    { "hn"  "H" "sp3" }
>>    { "ho"  "H" "sp3" }
>>    { "hp"  "H" "sp3" }
>>    { "hs"  "H" "sp3" }
>>    { "hw"  "H" "sp3" }
>>    { "hx"  "H" "sp3" }
>>    { "o"  "O" "sp2" }
>>    { "o2"  "O" "sp2" }
>>    { "oh"  "O" "sp3" }
>>    { "op"  "O" "sp3" }
>>    { "oq"  "O" "sp3" }
>>    { "os"  "O" "sp3" }
>>    { "ow"  "O" "sp3" }
>>    { "c"  "C" "sp2" }
>>    { "c1"  "C" "sp2" }
>>    { "c2"  "C" "sp2" }
>>    { "c3"  "C" "sp3" }
>>    { "ca"  "C" "sp2" }
>>    { "cc"  "C" "sp2" }
>>    { "cd"  "C" "sp2" }
>>    { "ce"  "C" "sp2" }
>>    { "cf"  "C" "sp2" }
>>    { "cg"  "C" "sp2" }
>>    { "ch"  "C" "sp2" }
>>    { "cp"  "C" "sp2" }
>>    { "cq"  "C" "sp2" }
>>    { "cu"  "C" "sp2" }
>>    { "cv"  "C" "sp2" }
>>    { "cx"  "C" "sp2" }
>>    { "cy"  "C" "sp2" }
>>    { "cz"  "C" "sp2" }
>>    { "n"   "N" "sp2" }
>>    { "n1"  "N" "sp2" }
>>    { "n2"  "N" "sp2" }
>>    { "n3"  "N" "sp3" }
>>    { "n4"  "N" "sp3" }
>>    { "na"  "N" "sp2" }
>>    { "nb"  "N" "sp2" }
>>    { "nc"  "N" "sp2" }
>>    { "nd"  "N" "sp2" }
>>    { "ne"  "N" "sp2" }
>>    { "nf"  "N" "sp2" }
>>    { "nh"  "N" "sp2" }
>>    { "ni"  "N" "sp2" }
>>    { "nj"  "N" "sp2" }
>>    { "nk"  "N" "sp3" }
>>    { "nl"  "N" "sp3" }
>>    { "nm"  "N" "sp2" }
>>    { "nn"  "N" "sp2" }
>>    { "no"  "N" "sp2" }
>>    { "np"  "N" "sp3" }
>>    { "nq"  "N" "sp3" }
>>    { "s"   "S" "sp2" }
>>    { "s2"   "S" "sp2" }
>>    { "s3"   "S" "sp3" }
>>    { "s4"   "S" "sp3" }
>>    { "s6"   "S" "sp3" }
>>    { "sh"   "S" "sp3" }
>>    { "sp"   "S" "sp3" }
>>    { "sq"   "S" "sp3" }
>>    { "ss"   "S" "sp3" }
>>    { "sx"   "S" "sp3" }
>>    { "sy"   "S" "sp3" }
>>    { "p2"   "P" "sp2" }
>>    { "p3"   "P" "sp3" }
>>    { "p4"   "P" "sp3" }
>>    { "p5"   "P" "sp3" }
>>    { "pb"   "P" "sp3" }
>>    { "pc"   "P" "sp3" }
>>    { "pd"   "P" "sp3" }
>>    { "pe"   "P" "sp3" }
>>    { "pf"   "P" "sp3" }
>>    { "px"   "P" "sp3" }
>>    { "py"   "P" "sp3" }
>>    { "f"   "F" "sp3" }
>>    { "cl"  "Cl" "sp3" }
>>    { "br"  "Br" "sp3" }
>>    { "i"   "I"  "sp3" }
>> }
>> #
>> #  Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff.dat
Loading parameters: /home/juliyan/Desktop/amber20_src/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
>
> loadamberprep cgu.prepin
Loading Prep file: ./cgu.prepin
Loaded UNIT: CGU
> loadamberparams frcmod2.cgu
Loading parameters: ./frcmod2.cgu
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamberparams frcmod1.cgu
Loading parameters: ./frcmod1.cgu
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> ost = loadpdb ost.pdb
Loading PDB file: ./ost.pdb
Matching PDB residue names to LEaP variables.
Mapped residue PRO, term: Terminal/beginning, seq. number: 0 to: NPRO.
Mapped residue ALA, term: Terminal/last, seq. number: 36 to: CALA.
  Added missing heavy atom: .R<CGU 5>.A<OXT 5>
  Added missing heavy atom: .R<CGU 9>.A<OXT 5>
  Added missing heavy atom: .R<CGU 12>.A<OXT 5>
  total atoms in file: 314
  Leap added 290 missing atoms according to residue templates:
       3 Heavy
       287 H / lone pairs
> check ost
Checking 'ost'....
Warning: The unperturbed charge of the unit (-2.003000) is not zero.
Warning: Close contact of 1.220 angstroms between nonbonded atoms HA and HB2
-------  .R<CGU 5>.A<HA 20> and .R<CGU 5>.A<HB2 18>
Warning: Close contact of 1.392 angstroms between nonbonded atoms HB3 and HG
-------  .R<CGU 5>.A<HB3 19> and .R<CGU 5>.A<HG 17>
Warning: Close contact of 1.279 angstroms between nonbonded atoms HB2 and HG
-------  .R<CGU 5>.A<HB2 18> and .R<CGU 5>.A<HG 17>
Warning: Close contact of 0.483 angstroms between nonbonded atoms HB2 and CA
-------  .R<CGU 5>.A<HB2 18> and .R<CGU 5>.A<CA 2>
Warning: Close contact of 0.476 angstroms between nonbonded atoms HG and CB
-------  .R<CGU 5>.A<HG 17> and .R<CGU 5>.A<CB 7>
Warning: Close contact of 1.279 angstroms between nonbonded atoms HXT and HA
-------  .R<CGU 5>.A<HXT 6> and .R<PRO 6>.A<HA 12>
Warning: Close contact of 0.452 angstroms between nonbonded atoms HXT and CA
-------  .R<CGU 5>.A<HXT 6> and .R<PRO 6>.A<CA 11>
Warning: Close contact of 1.012 angstroms between nonbonded atoms HXT and N
-------  .R<CGU 5>.A<HXT 6> and .R<PRO 6>.A<N 1>
Warning: Close contact of 1.419 angstroms between nonbonded atoms OXT and CA
-------  .R<CGU 5>.A<OXT 5> and .R<PRO 6>.A<CA 11>
Warning: Close contact of 0.054 angstroms between nonbonded atoms OXT and N
-------  .R<CGU 5>.A<OXT 5> and .R<PRO 6>.A<N 1>
Warning: Close contact of 1.341 angstroms between nonbonded atoms C and N
-------  .R<CGU 5>.A<C 3> and .R<PRO 6>.A<N 1>
Warning: Close contact of 1.365 angstroms between nonbonded atoms HA and HB2
-------  .R<CGU 9>.A<HA 20> and .R<CGU 9>.A<HB2 18>
Warning: Close contact of 1.339 angstroms between nonbonded atoms HB3 and HG
-------  .R<CGU 9>.A<HB3 19> and .R<CGU 9>.A<HG 17>
Warning: Close contact of 1.340 angstroms between nonbonded atoms HB2 and HG
-------  .R<CGU 9>.A<HB2 18> and .R<CGU 9>.A<HG 17>
Warning: Close contact of 0.467 angstroms between nonbonded atoms HB2 and CA
-------  .R<CGU 9>.A<HB2 18> and .R<CGU 9>.A<CA 2>
Warning: Close contact of 0.453 angstroms between nonbonded atoms HG and CB
-------  .R<CGU 9>.A<HG 17> and .R<CGU 9>.A<CB 7>
Warning: Close contact of 1.213 angstroms between nonbonded atoms HXT and HA
-------  .R<CGU 9>.A<HXT 6> and .R<VAL 10>.A<HA 4>
Warning: Close contact of 0.440 angstroms between nonbonded atoms HXT and CA
-------  .R<CGU 9>.A<HXT 6> and .R<VAL 10>.A<CA 3>
Warning: Close contact of 1.048 angstroms between nonbonded atoms HXT and N
-------  .R<CGU 9>.A<HXT 6> and .R<VAL 10>.A<N 1>
Warning: Close contact of 1.384 angstroms between nonbonded atoms OXT and CA
-------  .R<CGU 9>.A<OXT 5> and .R<VAL 10>.A<CA 3>
Warning: Close contact of 0.996 angstroms between nonbonded atoms OXT and H
-------  .R<CGU 9>.A<OXT 5> and .R<VAL 10>.A<H 2>
Warning: Close contact of 0.104 angstroms between nonbonded atoms OXT and N
-------  .R<CGU 9>.A<OXT 5> and .R<VAL 10>.A<N 1>
Warning: Close contact of 1.385 angstroms between nonbonded atoms C and H
-------  .R<CGU 9>.A<C 3> and .R<VAL 10>.A<H 2>
Warning: Close contact of 1.333 angstroms between nonbonded atoms C and N
-------  .R<CGU 9>.A<C 3> and .R<VAL 10>.A<N 1>
Warning: Close contact of 1.358 angstroms between nonbonded atoms HA and HB2
-------  .R<CGU 12>.A<HA 20> and .R<CGU 12>.A<HB2 18>
Warning: Close contact of 1.313 angstroms between nonbonded atoms HB3 and HG
-------  .R<CGU 12>.A<HB3 19> and .R<CGU 12>.A<HG 17>
Warning: Close contact of 1.338 angstroms between nonbonded atoms HB2 and HG
-------  .R<CGU 12>.A<HB2 18> and .R<CGU 12>.A<HG 17>
Warning: Close contact of 0.464 angstroms between nonbonded atoms HB2 and CA
-------  .R<CGU 12>.A<HB2 18> and .R<CGU 12>.A<CA 2>
Warning: Close contact of 0.444 angstroms between nonbonded atoms HG and CB
-------  .R<CGU 12>.A<HG 17> and .R<CGU 12>.A<CB 7>
Warning: Close contact of 1.219 angstroms between nonbonded atoms HXT and HA
-------  .R<CGU 12>.A<HXT 6> and .R<LEU 13>.A<HA 4>
Warning: Close contact of 0.430 angstroms between nonbonded atoms HXT and CA
-------  .R<CGU 12>.A<HXT 6> and .R<LEU 13>.A<CA 3>
Warning: Close contact of 1.064 angstroms between nonbonded atoms HXT and N
-------  .R<CGU 12>.A<HXT 6> and .R<LEU 13>.A<N 1>
Warning: Close contact of 1.364 angstroms between nonbonded atoms OXT and CA
-------  .R<CGU 12>.A<OXT 5> and .R<LEU 13>.A<CA 3>
Warning: Close contact of 1.026 angstroms between nonbonded atoms OXT and H
-------  .R<CGU 12>.A<OXT 5> and .R<LEU 13>.A<H 2>
Warning: Close contact of 0.106 angstroms between nonbonded atoms OXT and N
-------  .R<CGU 12>.A<OXT 5> and .R<LEU 13>.A<N 1>
Warning: Close contact of 1.280 angstroms between nonbonded atoms C and H
-------  .R<CGU 12>.A<C 3> and .R<LEU 13>.A<H 2>
Warning: Close contact of 1.328 angstroms between nonbonded atoms C and N
-------  .R<CGU 12>.A<C 3> and .R<LEU 13>.A<N 1>
Warning: Close contact of 1.471 angstroms between nonbonded atoms OE2 and HE2
-------  .R<GLU 19>.A<OE2 13> and .R<HIE 23>.A<HE2 13>
Warning: Close contact of 1.386 angstroms between nonbonded atoms HH12 and HD2
-------  .R<ARG 31>.A<HH12 19> and .R<ARG 32>.A<HD2 12>
Checking parameters for unit 'ost'.
Checking for bond parameters.
Error: Could not find bond parameter for: N - N
Error: Could not find bond parameter for: N - N
Error: Could not find bond parameter for: N - N
Checking for angle parameters.
Error: Could not find angle parameter: C - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: CT - N - N
Error: Could not find angle parameter: N - N - CT
Error: Could not find angle parameter: N - N - XC
Error: Could not find angle parameter: C - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: CT - N - N
Error: Could not find angle parameter: N - N - H
Error: Could not find angle parameter: N - N - XC
Error: Could not find angle parameter: C - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: H - N - N
Error: Could not find angle parameter: CT - N - N
Error: Could not find angle parameter: N - N - H
Error: Could not find angle parameter: N - N - XC
Warning: There are missing parameters.
check:  Warnings: 40
Unit is OK.
Exiting LEaP: Errors = 42; Warnings = 82; Notes = 0.
Thanks,
Kavinda
[NOTICE]
This e-mail and any attachments are confidential and intended only for the use of the addressee. They may contain information that is privileged or protected by copyright. If you are not the intended recipient, any dissemination, distribution, printing, copying or use is strictly prohibited. The University does not warrant that this e-mail and any attachments are secure and there is also a risk that it may be corrupted in transmission. It is your responsibility to check any attachments for viruses or defects before opening them. If you have received this transmission in error, please contact us on +6082 255000 and delete it immediately from your system. We do not accept liability in connection with computer virus, data corruption, delay, interruption, unauthorised access or unauthorised amendment.
Please consider the environment before printing this email.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!3pAZv5DWOavtNtdBG_S3Tz-xh2OPfGteJ286bC9XtMEJ-jDMs4B8IV8Nm0prNR9s8_47venLWKl_3aRogSazk9f8jIo$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!!KGKeukY!3pAZv5DWOavtNtdBG_S3Tz-xh2OPfGteJ286bC9XtMEJ-jDMs4B8IV8Nm0prNR9s8_47venLWKl_3aRogSazk9f8jIo$>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Mar 22 2024 - 00:00:02 PDT
Custom Search