Re: Re: Re: [AMBER] error in save prmtop

From: geyan <geyan.big.ac.cn>
Date: Tue, 23 Mar 2010 22:44:12 +0800

I got the prmtop file,but as you see,in the log file,I got these errors which made me unsure I'm right.
commands as follows,attached is the protein's structure and the log file.
> pro = loadpdb pro.pdb
> check pro
> addions pro Na+ 0
> solvateoct pro TIP3PBOX 9.0
> saveamberparm pro pro.top pro.crd
i still curious about what caused the looking error message?


2010-03-23



geyan



发件人: Carlos Simmerling
发送时间: 2010-03-23 22:33:38
收件人: AMBER Mailing List
抄送:
主题: Re: Re: [AMBER] error in save prmtop
 
no i don't think that is an error. are you sure you don't get a prmtop file?
maybe you can share your leap input with us.
On Tue, Mar 23, 2010 at 10:30 AM, geyan <geyan.big.ac.cn> wrote:
> thank you for your reply.
> this is the very end.so in your opinion,message says" Residues lacking
> connect0/connect1 -these don't have chain types marked:
> > res total affected
> > CGLN 1
> > NMET 1
> > WAT 7657
> > )
> > (no restraints)
> is not an error? if not,why does this happen?
> thanks
>
> 2010-03-23
>
>
>
> geyan
>
>
>
> 发件人: Carlos Simmerling
> 发送时间: 2010-03-23 22:24:59
> 收件人: AMBER Mailing List
> 抄送:
> 主题: Re: [AMBER] error in save prmtop
>
> i don't see an error. is this the end of the leap.log file?
> On Tue, Mar 23, 2010 at 10:04 AM, geyan <geyan.big.ac.cn> wrote:
> > hello everyone,I met the unexpected error in saving the prmtop,the
> detailed
> > information is as follows:
> >
> > Checking Unit.
> > ···················································
> > Not Marking per-residue atom chain types.
> > Marking per-residue atom chain types.
> > (Residues lacking connect0/connect1 -
> > these don't have chain types marked:
> > res total affected
> > CGLN 1
> > NMET 1
> > WAT 7657
> > )
> > (no restraints)
> >
> > I have searched this problem in google,but got no exact answers.Does
> > anybody met this error before?Is it a fatal problem for the latter
> > minimization and MD analyse?How can I figure out this error?Is it caused
> by
> > the PDB file of my protein structure?
> >
> > appreciated for anybody's help!
> >
> >
> >
> > 2010-03-23
> >
> >
> >
> > geyan
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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Received on Tue Mar 23 2010 - 08:00:07 PDT
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