AMBER Archive (2008)

Subject: AMBER: Amber heme parameters

From: Shaikh Abdul R S Ramaju (smasarsr_at_nus.edu.sg)
Date: Tue Oct 07 2008 - 01:31:34 CDT

Dear Amber Users,

I am new user to Amber. I am trying to prepare Amber input file for
Cytochrome P450. I am using contributed parameters available with the
Amber package. I have modified the prep file, replaced histidine with
Cysteine. HETATMs were replaced with ATOMs.

Also modified the pdb file similar to prep file. But while making the
input file for Amber using tleap, I am getting error message that there
is bond between Fe and C atom. Actually in the protein there is no bond
between Fe and backbone C atom of Cystein 357. Error message is attached
with this message.
I have attached all the necessary files, please have a look on it. It
will be very nice of you to tell me where it is done wrongly.
Thanks in advance.

Regards

Abdul Rajjak

National University of Singapore
Singapore

****************************************

> check mol
Checking 'mol'....
WARNING: There is a bond of 4.889570 angstroms between:
------- .R<HEM 357>.A<FE 9> and .R<HEM 357>.A<C 82>
ERROR: The unperturbed charge of the unit: -17.455300 is not integral.
WARNING: The unperturbed charge of the unit: -17.455300 is not zero.
Warning: Close contact of 2.246168 angstroms between .R<LEU 14>.A<HD13
13> and .R<LEU 14>.A<HA 4>
Warning: Close contact of 1.910426 angstroms between .R<ASN 33>.A<HD22
12> and .R<VAL 44>.A<HG12 9>
Warning: Close contact of 1.844847 angstroms between .R<GLN 39>.A<HE22
15> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.936478 angstroms between .R<GLN 39>.A<NE2
13> and .R<GLN 39>.A<H 2>
Warning: Close contact of 1.506529 angstroms between .R<GLU 40>.A<OE1
12> and .R<GLU 40>.A<H 2>
Warning: Close contact of 2.011145 angstroms between .R<GLU 40>.A<HG3
10> and .R<MET 336>.A<HE3 15>
Warning: Close contact of 2.195527 angstroms between .R<GLN 46>.A<O 17>
and .R<ARG 67>.A<HH22 22>
Warning: Close contact of 1.867627 angstroms between .R<ARG 67>.A<HH21
21> and .R<WAT 419>.A<H1 1>
Warning: Close contact of 2.178894 angstroms between .R<ARG 72>.A<HH11
18> and .R<ARG 72>.A<HG3 10>
Warning: Close contact of 2.219096 angstroms between .R<ASP 77>.A<HB2 6>
and .R<WAT 465>.A<H2 2>
Warning: Close contact of 1.687677 angstroms between .R<PRO 86>.A<O 14>
and .R<GLY 298>.A<H 2>
Warning: Close contact of 1.954963 angstroms between .R<ILE 88>.A<HD13
17> and .R<ILE 88>.A<H 2>
Warning: Close contact of 1.164720 angstroms between .R<TYR 96>.A<HH 15>
and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.153334 angstroms between .R<TYR 96>.A<HH 15>
and .R<THR 101>.A<OG1 11>
Warning: Close contact of 2.166421 angstroms between .R<TYR 96>.A<OH 14>
and .R<THR 101>.A<HG1 12>
Warning: Close contact of 1.140836 angstroms between .R<GLN 108>.A<HE22
15> and .R<GLN 108>.A<HB3 7>
Warning: Close contact of 1.850847 angstroms between .R<GLN 110>.A<HE22
15> and .R<ASN 229>.A<HA 4>
Warning: Close contact of 1.823980 angstroms between .R<ARG 112>.A<HH11
18> and .R<HEM 357>.A<O1D 80>
Warning: Close contact of 1.339097 angstroms between .R<GLN 117>.A<HE21
14> and .R<WAT 433>.A<H1 1>
Warning: Close contact of 1.452897 angstroms between .R<ASP 125>.A<HA 4>
and .R<WAT 496>.A<H2 2>
Warning: Close contact of 1.827194 angstroms between .R<ARG 130>.A<HD2
12> and .R<ARG 130>.A<HA 4>
Warning: Close contact of 1.762332 angstroms between .R<ILE 131>.A<HD13
17> and .R<ILE 162>.A<HD13 17>
Warning: Close contact of 1.785659 angstroms between .R<ALA 135>.A<HA 4>
and .R<WAT 506>.A<H1 1>
Warning: Close contact of 1.668065 angstroms between .R<SER 141>.A<HB3
7> and .R<WAT 457>.A<H1 1>
Warning: Close contact of 1.648441 angstroms between .R<GLN 145>.A<H 2>
and .R<WAT 448>.A<H2 2>
Warning: Close contact of 2.124973 angstroms between .R<GLY 146>.A<H 2>
and .R<WAT 448>.A<O 3>
Warning: Close contact of 1.092559 angstroms between .R<GLY 146>.A<H 2>
and .R<WAT 448>.A<H1 1>
Warning: Close contact of 1.790061 angstroms between .R<THR 151>.A<HG23
10> and .R<SER 258>.A<HG 9>
Warning: Close contact of 0.976382 angstroms between .R<THR 151>.A<HG21
8> and .R<THR 151>.A<H 2>
Checking parameters for unit 'mol'.
Checking for bond parameters.
Could not find bond parameter for: FE - C
Checking for angle parameters.
Could not find angle parameter: NO - FE - C
Could not find angle parameter: NP - FE - C
Could not find angle parameter: NO - FE - C
Could not find angle parameter: NP - FE - C
Could not find angle parameter: FE - C - O
Could not find angle parameter: FE - C - N
Could not find angle parameter: SH - FE - C
Could not find angle parameter: HC - CT - SH
Could not find angle parameter: HC - CT - SH
Could not find angle parameter: N - CT - HC
There are missing parameters.
check: Errors: 1 Warnings: 83






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