[gmx-users] [gmx-users]Violation of distance restraints

Mon Sep 8 10:05:01 CEST 2003

Hi Chris,

bondtype 5 (CONN_BONDS) will do the trick.

Good luck,

Gerrit
> 
> Dear gmx'ers,=20
> I am trying to use 7 spin relaxation NMR derived distance restraints =
> between atoms of a small organic molecule (substrate) and a protein to =
> refine a substrate-enzyme complex with MD. As a starting structure, I =
> use a automaticaly docked substrate pose in the protein binding pocket =
> which is more or less in agreement with these distance restraints.  =
> However, as the substrate and the protein are not considered as one =
> molecule,  the distance restraints are 'heavily violated' (31 nm!) as a =
> result of the fact that the substrate is 'placed outside' the protein =
> ('placed outside the box'), and the run crashes immediately.=20
> 
> I want to solve this problem by defining either one 'connection bond' or =
> one 'harmonic potential bond' (with a force constant of "0") between the =
> substrate and the protein (in addition to the distance restraints), =
> because I do not want to turn these bonds into constraints, and I do not =
>  want to define a 'chemical' bond between the protein and the substrate. =
> Which bond type should I use?=20
> 
> With kind regards and thanking you in advance,=20
> 
> Chris=20
>  =20
>  =20
> 
> --=20
> C. de Graaf, MSc=20
> 
> LACDR - Division of Molecular Toxicology=20
> Department of Pharmacochemistry,=20
> Vrije Universiteit,=20
> De Boelelaan 1083, 1081 HV Amsterdam
> 
> Tel. (31) 020-4447608
> Fax. (31) 020-4447610
> email: degraaf at few.vu.nl  
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> <DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
> size=3D3>Dear gmx'ers,=20
> </FONT>
> <P>I am trying to use 7 spin relaxation NMR derived distance restraints =
> between=20
> atoms of a small organic molecule (substrate) and a protein to refine a=20
> substrate-enzyme complex with MD. As a starting structure, I use a =
> automaticaly=20
> docked substrate pose in the protein binding pocket which is more or =
> less in=20
> agreement with these distance restraints.&nbsp; However, as the =
> substrate and=20
> the protein are not considered as one molecule,&nbsp; the distance =
> restraints=20
> are 'heavily violated' (31 nm!) as a result of the fact that the =
> substrate is=20
> 'placed outside' the protein ('placed outside the box'), and the run =
> crashes=20
> immediately.=20
> <P>I want to solve this problem by defining either one 'connection bond' =
> or one=20
> 'harmonic potential bond' (with a force constant of "0") between the =
> substrate=20
> and the protein (in addition to the distance restraints), because I do =
> not want=20
> to turn these bonds into constraints, and I do not&nbsp; want to define =
> a=20
> 'chemical' bond between the protein and the substrate. Which bond type =
> should I=20
> use?=20
> <P>With kind regards and thanking you in advance,=20
> <P>Chris <BR>&nbsp; <BR>&nbsp; <PRE>--&nbsp;
> C. de Graaf, MSc&nbsp;
> 
> LACDR - Division of Molecular Toxicology&nbsp;
> Department of Pharmacochemistry,&nbsp;
> Vrije Universiteit,&nbsp;
> De Boelelaan 1083, 1081 HV Amsterdam
> 
> Tel. (31) 020-4447608
> Fax. (31) 020-4447610
> email: degraaf at few.vu.nl</PRE>&nbsp; </FONT></DIV></BODY></HTML>
> 
> ------=_NextPart_000_0035_01C375EF.680A39C0--
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