nikhil damle wrote:
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 ?
http://oldwiki.gromacs.org/index.php/Tutorials#General
The "drug-enzyme complex" tutorial will tell you how to do this. You won't need
to use PRODRG, as the tutorial does, since you have already generated your
topologies with pdb2gmx. But everything else is still applicable.
-Justin
------------------------------------------------------------------------
*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
<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 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> <mailto: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> <mailto: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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Cricket on your mind? Visit the ultimate cricket website. Enter now!
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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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