[gmx-users] Pdb for urea crystal

Sivashangari Gnanasambandam g0501135 at nus.edu.sg
Wed Nov 1 11:45:01 CET 2006


I tried with 8 molecules . But it shows the following error,
Invalid order for directive moleculetype, file ""/usr/local/gromacs/share/gromacs/top/spc.itp"", line 1 

Suggest me the correction.
Thank you

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of merc mertens
Sent: Wednesday, November 01, 2006 5:58 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Pdb for urea crystal


your gro contains 8 urea molecules and your top only one. you should change the line " UREA             1" in your "[ molecules ]"-section to " UREA             8".


-------- Original-Nachricht --------
Datum: Wed, 1 Nov 2006 17:46:59 +0800
Von: "Sivashangari Gnanasambandam" <g0501135 at nus.edu.sg>
An: gmx-users at gromacs.org
Betreff: [gmx-users] Pdb for urea crystal

> Hi,
>  <<one.gro>>  <<one.pdb>>  <<one.top>> I am very new to the GROMACS 
> and I couldn't able to proceed further from converting a pdb file to 
> gro file for one month.
> I tried to create topology file using the format suggested in mailing 
> list but it shows the error '' No of coordinates in gro file does not 
> match with topology'. I attached my gro and top file for your reference.
> Kindly help me to come out from my problem.
> Thank you
> Shankari

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