VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Sep 21 2006 - 17:42:35 CDT

Ah, I just noticed you generated the file with Sybyl.

You will need then to work on the pdb a little first. You need to
rename the AMN to LYS (and AMD to LYS) and set their residue numbers
to the one after (and before). Termini should not be their own
residue, they belong with the residue they are part of. So really,
you only have residues 1 - 11.

On Sep 21, 2006, at 4:22 PM, Al-Rawi, Ahlam wrote:

> Hi JC,
> Thanks for your reply. I tried
>
> package require psfgen
> topology top_all27_prot_lipid.inp
> pdbalias residue HIS HSE
> pdbalias atom ILE CD1 CD
> segment P1 {
> pdb beta1.pdb
> first NTER
> last CT2
> }
> coordpdb beta1.pdb P1
> guesscoord
> writepdb betaout.pdb
> writepsf betaout.psf
> exit
>
> But it is not working. Can you please
> tell me if I am make mistakes.
> Thanks so much
> Ahlam
> Ahlam Al-Rawi
> Physics Department
> Kansas State University
> 785-532-5520
> cell 785-317-5858
>
>
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu on behalf of JC Gumbart
> Sent: Wed 9/20/2006 2:43 PM
> To: Al-Rawi, Ahlam
> Cc: VMD List
> Subject: Re: vmd-l: psf for protein
>
> I am not sure why you are renaming the residues, or making them
> different numbers. What you want, I think, are actually just
> standard types of termini. Without any modification of the pdb
> necessary (no deleting atoms, renumbering, etc.), you should be able
> to define your segment something like this:
>
> segment A {
> first NTER
> last CT2
> pdb beta.pdb
> }
>
> and then after the rest of your commands, it should come out fine.
>
> Look at the definitions in the topology file for more information;
> also the psfgen user's manual has good tips: http://www.ks.uiuc.edu/
> Research/vmd/plugins/psfgen/
>
> Let us know if that does what you want.
>
> On Sep 19, 2006, at 12:03 PM, Al-Rawi, Ahlam wrote:
>
>> I atached my pdb files,beta1.pdb is the original file beta.pdb the
>> one that I chang.
>> Yes it has the bond and I did change this pdb file so that RESI(0)
>> +RESI(1) become RESI AHS
>> The missing bound is between RESI (AHS) AND RESI (LYS 2) and LYS(10)
>> and (AHE).
>> I need to know how I let the topology file think that AHS and AHE
>> is conected to the rest.
>> Thanks
>> Ahlam
>>
>> Ahlam Al-Rawi
>> Physics Department
>> Kansas State University
>> 785-532-5520
>> cell 785-317-5858
>>
>>
>>
>> -----Original Message-----
>> From: JC Gumbart [mailto:gumbart_at_ks.uiuc.edu]
>> Sent: Tue 9/19/2006 10:43 AM
>> To: Al-Rawi, Ahlam
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: psf for protein
>>
>> Does your pdb have the bond before you run psfgen? And do you load
>> the psf and then load the pdb into VMD? Also, which bond is missing?
>>
>> I expect any more information you could provide would be helpful in
>> this case.
>>
>>
>> On Sep 18, 2006, at 5:24 PM, Al-Rawi, Ahlam wrote:
>>
>>>
>>> Dear All,
>>> I am preparing a psf for a Beta sheet protein that start with NH3
>>> then KKK and at the end it has KKK and (C=O NH2)
>>> The results pdb file has a missing bond and I have no idea why??
>>> In the topology file :
>>>
>>> **I added the NH3 to the first LYS after removing the NH and then I
>>> call it AHS
>>> **and I renamed the last LYS to ASE after removing the C=O
>>> **The last molecules I add it as a new residue contain(C=O and NH2)
>>> I need to know why I have the missing bond when I view the pdb file
>>> in vmd.
>>> Thanks,
>>> Ahlam
>>> Ahlam Al-Rawi
>>> Physics Department
>>> Kansas State University
>>> 785-532-5520
>>> cell 785-317-5858
>>>
>>
>>
>>
>> <beta1.pdb>
>
>
>
> <beta1.pdb>