Re: Analysis of NAMD output with CHARMM

From: Nathalie Reuter (Nathalie.Reuter_at_bccs.uib.no)
Date: Mon Feb 14 2005 - 09:51:07 CST

Hi,

if you have a linux machine, Nedit is probably installed by default. It
is a text editor that allows you to work easily on columns.

If this does not work, you should try to make Charmm read your pdb file
using:

-----------
open unit 1 card read name "myfile.pdb"
read sequ pdb unit 1
close unit 1

! read in pdb coordinate file
open unit 1 form read name "../coor/pr3.pdb"
read coor pdb unit 1
close unit 1

print coor
-------

Just to make sure the error comes from the PDB.

Nathalie

Leyla Celik wrote:

>Hi,
>
>I am not all that efficient at NAMD yes... What is "nedit" and how do I use it?
>
>/Leyla
>
>
>Citat Gianluca Interlandi <gianluca_at_bioc.unizh.ch>:
>
>
>
>>Hi Nathalie,
>>
>>It seems that CHARMM doesn't read the residue number correctly:
>>
>>
>>
>>>** WARNING ** For atom in coordinate file, could not find residue in PSF,
>>>and
>>>is thus ignored:
>>>
>>> SEGID=WT1 RESID=000 RESNAME= TIP3 TYPE= H1
>>>*** LEVEL 1 WARNING *** BOMLEV IS -3
>>>
>>>
>>I mean "RESID=000" in the fifth line above points out that the columns in
>>the pdb are somehow shifted, exaclty as you mention in your last e-mail.
>>You can use "nedit" to move the columns to the place where they should be.
>>However, to avoid that nedit replaces empty spaces with tabs you must
>>select Preferences -> Tabs and unselect "Use tab characters in padding and
>>emulated tabs".
>>
>>There must be a more elegant way, but maybe this can help you.
>>
>>Best, Gianluca
>>
>>----------------------------------------------------
>>Gianluca Interlandi gianluca_at_bioc.unizh.ch
>> +41 (0) 1 635 55 93
>> +41 (0)79 655 73 35
>> http://biocroma.unizh.ch/gianluca/
>>
>>PhD-Student of the Department of Biochemistry
>>at the University of Zurich Irchel, Switzerland
>>-----------------------------------------------------
>>
>>
>>
>
>
>
>

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