[gmx-users] simulation of protein in presence of ATP

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 23 17:30:40 CEST 2009 


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 <jalemkul at vt.edu>
> *To:* Discussion list for GROMACS users <gmx-users at 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.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
>  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at 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.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au> <mailto:Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>>
>  >  > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org 
> <mailto:gmx-users at 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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-- 
========================================

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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