Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Jun 11 2010 - 12:23:03 CDT

You have a couple problems with your Molden-generated pdb. First, the resname is "2", but should be "CELLUBO" (you also need to be sure that a resname that long is allowed). Also, all the atom names are generic. You need to carefully assign atoms names according to their names in the topology file, using VMD for example.

Good luck!

On Jun 10, 2010, at 3:04 PM, Bharath Rajeswaran wrote:

> Hi sir,
>
> This is the file. cellubo.pdb is the pdb file and using psfgen. I am sending it sir. I tried reading the meaning of the error. I am not able to figure out what molecule missing or residue unknown meaning. When I try with a protein , it works fine. But with sugars, i am not able to figure out.
>
> Thanks a lot sir
> Bharath.R
>
> On 11 June 2010 01:19, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Can you also send cellubo1.pdb?
>
>
> On Jun 10, 2010, at 11:25 AM, Bharath Rajeswaran wrote:
>
>> Hi,
>>
>> I am trying to do a simulation for a polymer of glucose. I used the corresponding patches to set up the topology file of the sugar molecule. I got the pdb and used molden to write the pdb for the atoms set that I am considering. I however get the following error. Can someone help me out?
>>
>>
>> Created by CHARMM version 34 1
>> duplicate residue key 14BB will be ignored
>> building segment U
>> reading residues from pdb file cellubo1.pdb
>> unknown residue type 2
>> extracted 1 residues from pdb file
>> Info: generating structure...
>> unknown residue type 2
>> ERROR: failed on end of segment
>> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
>>
>> MOLECULE MISSING! Use resetpsf to start over.
>>
>> MOLECULE MISSING! Use resetpsf to start over.
>>
>> My system is cellubiose and I am sending topology file that I modified. What is this error unknown residue type 2 .
>>
>> Thanks
>>
>> Regards
>> Bharath Rajeswaran <top_all36_carb.odt>
>
>
> <cellubopdb.odt><cellubo1pdb.odt>

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