Dear Amber users
I am trying to parametrize ligand of my system as follows:-
source leaprc.protein.ff14SB
source leaprc.gaff2
source leaprc.water.tip3p
loadoff BG6.lib
loadamberprep BG6.prepi
loadamberparams BG6.frcmod
protein = loadpdb Combined_lig.pdb
check protein
solvateBox protein TIP3PBOX 14.0 iso
addIonsRand protein Na+ 0
saveamberparm protein complex_BG6.prmtop complex_BG6.inpcrd
quit
It saves parameters however it gives warnings such as for all aminoacids in
protein it says Nonterminal, was not found in name map when I load protein
pdb file as below:-
> protein = loadpdb Combined_lig.pdb
Loading PDB file: ./Combined_lig.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
Mapped residue VAL, term: Terminal/beginning, seq. number: 0 to: NVAL.
(Residue 1: GLN, Nonterminal, was not found in name map.)
(Residue 2: SER, Nonterminal, was not found in name map.)
(Residue 3: ASP, Nonterminal, was not found in name map.)
(Residue 4: THR, Nonterminal, was not found in name map.)
Also
when I perform check protein it gives:-
> check protein
Checking 'protein'....
WARNING: The unperturbed charge of the unit: -3.999999 is not zero.
Warning: Close contact of 1.285552 angstroms between .R<NVAL 27>.A<H1 2>
and .R<GLN 28>.A<H 2>
Warning: Close contact of 1.469967 angstroms between .R<ILE 35>.A<HD13 17>
and .R<ILE 35>.A<H 2>
Warning: Close contact of 1.475518 angstroms between .R<TYR 70>.A<HH 15>
and .R<SER 117>.A<HB3 7>
Warning: Close contact of 1.089533 angstroms between .R<SER 106>.A<HG 9>
and .R<HIE 124>.A<HE2 13>
Warning: Close contact of 1.340599 angstroms between .R<GLN 111>.A<H 2> and
.R<SER 117>.A<HG 9>
Warning: Close contact of 1.470486 angstroms between .R<SER 123>.A<HA 4>
and .R<ASN 126>.A<HD22 12>
Warning: Close contact of 1.404432 angstroms between .R<ILE 168>.A<HD12 16>
and .R<VAL 444>.A<HG12 9>
Warning: Close contact of 1.483634 angstroms between .R<LEU 177>.A<H 2> and
.R<THR 466>.A<HG1 12>
Warning: Close contact of 1.465392 angstroms between .R<GLN 178>.A<HE22 15>
and .R<GLN 178>.A<H 2>
Warning: Close contact of 1.362380 angstroms between .R<ILE 187>.A<HD12 16>
and .R<ILE 196>.A<HD11 15>
Warning: Close contact of 1.409726 angstroms between .R<GLN 209>.A<HE21 14>
and .R<ARG 439>.A<HD2 12>
Warning: Close contact of 1.372477 angstroms between .R<ASN 218>.A<HD22 12>
and .R<PHE 221>.A<HD2 18>
Warning: Close contact of 1.477970 angstroms between .R<ASN 226>.A<HD22 12>
and .R<ASN 229>.A<HD22 12>
Warning: Close contact of 1.352249 angstroms between .R<ARG 227>.A<HH11 18>
and .R<ARG 227>.A<HG3 10>
Warning: Close contact of 1.145831 angstroms between .R<ARG 227>.A<HE 15>
and .R<ASP 350>.A<HB3 7>
Warning: Close contact of 1.270782 angstroms between .R<CYS 232>.A<HG 9>
and .R<PHE 501>.A<HB2 6>
Warning: Close contact of 1.454106 angstroms between .R<PRO 240>.A<HD2 3>
and .R<PHE 241>.A<HD1 10>
Warning: Close contact of 0.970063 angstroms between .R<THR 243>.A<HG21 8>
and .R<TYR 308>.A<HH 15>
Warning: Close contact of 1.184614 angstroms between .R<THR 243>.A<H 2> and
.R<TYR 308>.A<HH 15>
Warning: Close contact of 1.409402 angstroms between .R<ARG 246>.A<HG3 10>
and .R<ARG 246>.A<H 2>
Warning: Close contact of 1.001470 angstroms between .R<MET 260>.A<HE1 13>
and .R<PHE 465>.A<HE1 12>
Checking parameters for unit 'protein'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 31
Unit is OK.
How can I solve these problems? I have attached leap.log file as attachment.
thank you
Sadaf
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Received on Mon Jul 15 2019 - 13:30:02 PDT
