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 <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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 <[email protected]
<mailto:[email protected]>>
> *To:* Discussion list for GROMACS users <[email protected]
<mailto:[email protected]>>
> *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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