Re: RetinalTop

From: Bjoern Olausson (namdlist_at_googlemail.com)
Date: Tue Aug 03 2010 - 02:57:26 CDT

On Tuesday 03 August 2010 05:53:13 Ale Gomez wrote:
> I really appreciate your help Basak!
> I started all over again including your suggestions and untill now looks
> fine. I am only concern about one warming in log file during the first
> "step", when only lipid tails are free to move. I get this message:
>
> Warning: VDW TYPE NAME CR15 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR14 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR13 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR12 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR11 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR10 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR9 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR8 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR7 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR6 MATCHES PARAMETER TYPE NAME CR*
> Warning: VDW TYPE NAME CR5 MATCHES PARAMETER TYPE NAME CR*
>
I guess these warnings will only "WARN" you, that a bunch of Atoms match
single parameter and you should check if this is what you want.

CR* 0.000000 -0.110000 2.100000 0.000 -0.110000 1.600000 !last 2 v14
                ! RETINAL from ab initio calc's (J. Baudry) Sept. 1996

> Warning: Ignored 444 bonds with zero force constants.
> Warning: Will get H-H distance in rigid H2O from H-O-H angle.
>
You are probably using SHAKE ('rigidbonds water' or 'rigidbonds all') thus 444
should be equal the number of TIP3 waters in your system.
Nothing to concern about.

Cheers
Bjoern

-- 
Bjoern Olausson
Martin-Luther-Universitšt Halle-Wittenberg 
Fachbereich Biochemie/Biotechnologie
Kurt-Mothes-Str. 3
06120 Halle/Saale
Phone: +49-345-55-24942

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