Re: Hoe to create psf file of C-terminous of protein?

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 19:49:33 CDT

You have to make separate pdbs for each chain in your system. When
you say the chain after ASN, do you mean another protein? ATP? In
any case, write out separate pdbs for each of these and then use
multiple segment and coordpdb commands in your script to generate the
psf.

i.e.

segment A {pdb A.pdb
..
}
coordpdb A.pdb A

segment B {pdb B.pdb
..
}
coordpdb B.pdb B

On Aug 14, 2007, at 7:07 PM, Qiang Zhong wrote:

> Thank you very much! I have change .pgn as you say, but error is
> still there,
> Then I delete the chain after ASN, Then I find it is correct. So I
> want to know
> whether there are another method to solve it?
>
>
> 在您的来信中曾 提到:
>> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
>> Reply-To:
>> To: Qiang Zhong <zqiang320_at_webmail.hzau.edu.cn>
>> Subject: Re: namd-l: Hoe to create psf file of C-terminous of
>> protein?
>> Date:Tue, 14 Aug 2007 09:00:20 -0500
>>
>> You're running across two issues:
>> -You didn't specify that a C terminal patch should be applied. You
>> either need to have automatic patching defined in your topology
>> file, or
>> define the segment as, eg,
>>
>> segment BH {
>> pdb XXX_ATP.pdb
>> first NTER
>> last CTER
>> }
>>
>>
>> to apply N-terminal and C-terminal patches
>>
>> -The warnings you got are likely because your input pdb doesn't
>> follow
>> charmm naming conventions: the carbonyl oxygen on the last residue is
>> named OXT, not O. You either need to rename it or alias it.
>>
>> Peter
>>
>>
>> Qiang Zhong wrote:
>>> Dear NAMD Users:
>>> I have a complex of protein and ATP, when I create psf
>>> file of
> complex,
>>> I got error message:
>>>
>>> ERROR: Missing atoms for bond C(0) N(1) in residue ASN:309
>>> ERROR: Missing atoms for improper C(0) CA(0) N(1) O(0)
>>> in residue ASN:309
>>> ERROR: Missing atoms for cross-term C(-1) N(0) CA(0) C(0) N(0) CA
>>> (0) C(0)
> N(1)
>>> in residue ASN:309
>>>
>>> where ASN is C-terminous residue of protein,The pdb file of ASN is:
>>>
>>> ATOM 2391 N ASN B 309 -25.381 -30.889 6.595 1.00 68.77
> N
>>>
>>> ATOM 2392 CA ASN B 309 -26.117 -30.619 5.364 1.00 70.45
> C
>>>
>>> ATOM 2393 C ASN B 309 -27.266 -29.640 5.606 1.00 71.44
> C
>>>
>>> ATOM 2394 CB ASN B 309 -26.707 -31.905 4.757 1.00 70.80
> C
>>>
>>> ATOM 2395 CG ASN B 309 -25.639 -32.782 4.129 1.00 71.07
> C
>>>
>>> ATOM 2396 OD1 ASN B 309 -25.211 -32.577 3.000 1.00 70.80
> O
>>>
>>> ATOM 2397 ND2 ASN B 309 -25.236 -33.789 4.922 1.00 70.60
> N
>>>
>>> ATOM 2398 OXT ASN B 309 -27.900 -29.717 6.659 1.00 0.00
> O
>>>
>>> The output ASN in the output pdb is:
>>> ATOM 4731 N ASN B 309 -25.381 -30.889 6.595 1.00
>>> 0.00 BH
> N
>>> ATOM 4732 HN ASN B 309 -25.920 -30.790 7.430 0.00
>>> 0.00 BH
> H
>>> ATOM 4733 CA ASN B 309 -26.117 -30.619 5.364 1.00
>>> 0.00 BH
> C
>>> ATOM 4734 HA ASN B 309 -25.410 -30.137 4.697 0.00
>>> 0.00 BH
> H
>>> ATOM 4735 CB ASN B 309 -26.707 -31.905 4.757 1.00
>>> 0.00 BH
> C
>>> ATOM 4736 HB1 ASN B 309 -27.192 -32.477 5.578 0.00
>>> 0.00 BH
> H
>>> ATOM 4737 HB2 ASN B 309 -27.493 -31.656 4.015 0.00
>>> 0.00 BH
> H
>>> ATOM 4738 CG ASN B 309 -25.639 -32.782 4.129 1.00
>>> 0.00 BH
> C
>>> ATOM 4739 OD1 ASN B 309 -25.211 -32.577 3.000 1.00
>>> 0.00 BH
> O
>>> ATOM 4740 ND2 ASN B 309 -25.236 -33.789 4.922 1.00
>>> 0.00 BH
> N
>>> ATOM 4741 HD21 ASN B 309 -24.527 -34.394 4.569 0.00
>>> 0.00 BH
> H
>>> ATOM 4742 HD22 ASN B 309 -25.622 -33.890 5.834 0.00
>>> 0.00 BH
> H
>>> ATOM 4743 C ASN B 309 -27.266 -29.640 5.606 1.00
>>> 0.00 BH
> C
>>> ATOM 4744 O ASN B 309 -26.897 -28.712 5.658 0.00
>>> 0.00 BH
> O
>>>
>>> I know it is not correct, because it is not realy C-terminous style.
>>>
>>> In my pgn file:
>>>
>>> package require psfgen
>>>
>>> topology top_all27_prot_na_ppi_thp.inp
>>>
>>> pdbalias residue HIS HSE
>>>
>>> pdbalias atom ILE CD1 CD
>>>
>>> segment BH {pdb XXX_ATP.pdb}
>>>
>>> coordpdb XXX_ATP.pdb BH
>>>
>>> guesscoord
>>>
>>> writepdb XXXATP.pdb
>>>
>>> writepsf XXXATP.psf
>>>
>>> Could somebody tell me how to solve this problem? Thank you very
>>> much!
>>>
>>>
>>
>

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