OK till here done ! the pdb file generated for EM should have ATP molecule
@proper position as input .top file has the ATP.itp included. It did not have.
If I do -ci it would randomly replace the solvent. I want ATP @ its proper
location. how do i do this ?
________________________________
From: Justin A. Lemkul <jalem...@vt.edu>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Sent: Tuesday, 23 June, 2009 4:41:22 PM
Subject: Re: [gmx-users] simulation of protein in presence of ATP
nikhil damle wrote:
> Thanks a lot for kind help. I reached till grompp before minimizing energy of
> the system where I received an error msg as "Invalid order for directive
> defaults: ............filename........; line x" !!! what is the meaning of
> this error ? Is it something to do with path variable problem or writing
> things in improper order ?
>
Probably, if you've processed your protein with pdb2gmx as well as the ATP
molecule, you have two .top files, each of which contains an #include statement
for your force field, so you're duplicating these entries.
Without any information about the contents of your .top(s) or how you've
actually built things, this is just a guess.
See here:
http://oldwiki.gromacs.org/index.php/Errors#Invalid_order_for_directive_defaults
-Justin
> Nikhil
>
> ------------------------------------------------------------------------
> *From:* Mark Abraham <mark.abra...@anu.edu.au>
> *To:* Discussion list for GROMACS users <gmx-users@gromacs.org>
> *Sent:* Tuesday, 23 June, 2009 12:35:12 PM
> *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
>
> nikhil damle wrote:
> > Hi,
> > We can use max 4 coloumns for naming atoms. But .rtp file has 5
> coloumn atom names (AO1PG etc) That i modified to 4 letter name. But now the
> error is "atom N not found in residue 1ATP while combining tdb and rtp"
>
> pdb2gmx tries to cap termini of peptides automatically, but this isn't a
> peptide. So look at pdb2gmx -h and choose the option that will allow you to
> interactively choose that no terminal capping needs to take place.
>
> Mark
>
> > ------------------------------------------------------------------------
> > *From:* Mark Abraham <mark.abra...@anu.edu.au
> <mailto:mark.abra...@anu.edu.au>>
> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org
> <mailto:gmx-users@gromacs.org>>
> > *Sent:* Tuesday, 23 June, 2009 11:16:26 AM
> > *Subject:* Re: [gmx-users] simulation of protein in presence of ATP
> >
> > nikhil damle wrote:
> > > Hi,
> > >
> > > Thanks a lot for the reply. I am submitting ATP crds as ATP.pdb to
> pdb2gmx and receive the error as "No atoms found in pdb file ATP.pdb" I
> converted HETATM tag to ATOM tag. Still same error msg. Please find ATP.pdb
> file attached herewith.
> >
> > You've broken the PDB format, which encodes the information in
> fixed-column style. See http://www.wwpdb.org/documentation/format32/v3.2.html
> >
> > Mark
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-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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