AMBER Archive (2009)

Subject: Re: Re: [AMBER] error in AMBer distance constraint

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Oct 27 2009 - 06:28:22 CDT

can you send email with the mdin file and the dis.RST file included (as
text, not attachments)?
also put the beginning of the md.out file (the aprt up until the first
energy report).
it's really hard to say what's going on without seeing your inputs and
knowing what you tried.

2009/10/26 xuemeiwang1103 <xuemeiwang1103_at_163.com>

>
>
>
>
>
> 在2009-10-26，"Carlos Simmerling" <carlos.simmerling_at_gmail.com> 写道：
> >is that "NMR DIDISTANTENT.FILE" in the input? I think you want to put the
> >restraint into a separate file, the one called dis.RST.
> >are you following a tutorial or sample file?
> >
> >2009/10/25 xuemeiwang1103 <xuemeiwang1103_at_163.com>
> >
> >> Hi,
> >> I want constrain a distance in my system, but when I ran the input file,
> >> there are some errors in my output file. here is my input file:
> >> &cntrl
> >> imin=1,maxcyc=10000,ncyc=2000,
> >> ntb=1,igb=0,ntr=1,
> >> cut=8.0,
> >> ntpr=100,
> >> nmropt=1,
> >> &end
> >> &wt type='REST',istep1=1,istep2=10000,
> >> value1=1.0,
> >> value2=1.0,&end
> >> &wt type='END'/
> >> LISTOUT=RST.OUT
> >> DISANG=dis.RST
> >> NMR DISTANTENT.FILE
> >> &rst iat= 9292, 7786, r1= 1.5, r2= 2.5, r3 = 3.0, r4 = 5.0, rk2=10.0,
> >> rk3=10.0, ir6=1, /
> >> &ENd
> >> and here is errors in my out put file:
> >> 5. REFERENCE ATOM COORDINATES
> >>
> >>
> >> ----- READING GROUP 1; TITLE:
> >> NMR DISTANTENT.FILE
> >>
> >> rfree: Error decoding variable 1 3 from:
> >> &rst
> >> this indicates that your input contains
> >>
> >> incorrect information
> >>
> >> field 1 was supposed to
> >> have a (1=character, 2=integer, 3=decimal) value
> >>
> >> I hope that someone can help me to deal with this trouble, thank you!!!
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER_at_ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >_______________________________________________
> >AMBER mailing list
> >AMBER_at_ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
> Hello Dr.Calors:
> Thank you for your papid reply ! There is a seperate dis.RST file . The
> error seems my input is in wrong form,and was not calculated at all.The
> Dr.Ross advised me in ASCII code ,I did't comprehend it fully ,is it so
> complex to do a distance restraint?
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> AMBER_at_ambermd.org
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>
>
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