AMBER Archive (2008)

Subject: RE: AMBER: Amber heme parameters

From: Shaikh Abdul R S Ramaju (smasarsr_at_nus.edu.sg)
Date: Wed Oct 08 2008 - 01:38:59 CDT

Hello Dr. Tian,

Thanks for reply.
It is working now.

Regards
Abdul Rajjak

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of sobereva
Sent: Tuesday, October 07, 2008 10:02 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Amber heme parameters

Hi

You can use "deletebond" and "bond" command to change
connecting relationship of atoms.

--Lu Tian

--- Shaikh Abdul R S Ramaju <smasarsr_at_nus.edu.sg>
wrote:

> 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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