From: pijush.ghosh_at_ndsu.edu
Date: Sun May 29 2005 - 15:50:15 CDT
Chen
Exactly,thats what i am also thinking, you can use GVIM editor, which
can help you in this find and replace job very easily, you can use other
editor also as you feel convenient. Make sure you make the necessary
changes in the corresponding places, and thats for sure is going to take
care of your problem. Try to restrict your segment name to three
alphabets.
I am sure you are going to smile soon.
GoodLuck.
Pijush.
> It looks like you need to go through and rename some of them.
> Your editor's "find and replace" command would come in handy here.
> This should only take a few minutes.
>
> Cheers,
>
> Mike
> On May 28, 2005, at 18:42, Wei Chen wrote:
>
>> Hi, Pijush,
>>
>> The problem is that there are duplicate residue id# (like 100I,
>> 100J,etc) in
>> the original pdb file. So when I use psfgen to generate the psf file,
>> only
>> one is kept.
>>
>> Look below: TYR is 100I, AlA is 100J, etc.
>>
>> Only TYR can be kept in generated psf file.
>>
>>> ATOM 3039 N TYR B 100I
>>> ATOM 3040 CA TYR B 100I
>>> ATOM 3041 C TYR B 100I
>>> ATOM 3042 O TYR B 100I
>>> ATOM 3043 CB TYR B 100I
>>> ATOM 3044 CG TYR B 100I
>>> ATOM 3045 CD1 TYR B 100I
>>> ATOM 3046 CD2 TYR B 100I
>>> ATOM 3047 CE1 TYR B 100I
>>> ATOM 3048 CE2 TYR B 100I
>>> ATOM 3049 CZ TYR B 100I
>>> ATOM 3050 OH TYR B 100I
>>> ATOM 3051 H TYR B 100I
>>> ATOM 3052 HH TYR B 100I
>>> ATOM 3053 N ALA B 100J
>>> ATOM 3054 CA ALA B 100J
>>> ATOM 3055 C ALA B 100J
>>> ATOM 3056 O ALA B 100J
>>> ATOM 3057 CB ALA B 100J
>>> ATOM 3058 H ALA B 100J
>>> ATOM 3059 N MET B 100K
>>> ATOM 3060 CA MET B 100K
>>> ATOM 3061 C MET B 100K
>>> ATOM 3062 O MET B 100K
>>> ATOM 3063 CB MET B 100K
>>> ATOM 3064 CG MET B 100K
>>> ATOM 3065 SD MET B 100K
>>> ATOM 3066 CE MET B 100K
>>> ATOM 3067 H MET B 100K
>>
>> Thanks!
>>
>> Wei Chen
>>
>>
>>
>>
>>
>>
>>
> --
> C. Michael McCallum
> http://chemistry.cop.uop.edu/cmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> (209) 946-2607 fax
>
>
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