Re: distorsion in hydrogens added

Date: Wed Nov 22 2006 - 12:18:15 CST


  thank you for your recomendation. I was using an old topology file
  (from a tutorial), and with the new version I have solved the problems
  with the LEU. Anyway, the hydrogens for PRO continue being
distorted. Do you have any idea why the problem continues for this

  Best wishes,

  Rebeca García Fandiño
  Postdoctoral student
  Parc Cientific de Barcelona (Spain)

  Citando Jerome Henin <>:

> Rebeca,
> IN your file, all leucine HGs have wrong coordinates. This problem has
> happened before, Peter Freddolino explains it there:
> Using recent CHARMM topology files (c31b1 and following) with the latest
> version of psfgen should give a good result.
>> Jerome
>> On Tuesday 21 November 2006 14:39, wrote:
>>> Hello,
>>> the main problems are in the residue "PRO", here the angles are really
>>> distorted in some cases.
>>> I send you a pdb of my protein after creating the psf.
>>> What is also really extrange is that a minimization of the protein
>>> does not correct the hydrogens in these residues, being the resultant
>>> structure perfectly stable.
>>> In response to your question, psfgen does not print any warning in the
>>> generation of the structure
>>> Thanks a lot for your help
>>> Rebeca García Fandiño
>>> Postdoctoral student
>>> Parc Cientific de Barcelona (Spain)
>>> Citando Jerome Henin <>:
>>>> Hi,
>>>> Are all hydrogens wrong or just a few? In what residues?
>>>> Also, does psfgen print warnings or errors when generating the structure?
>>>> It might also be helpful if you post a small gzipped pdb file
>>>> containing, say,
>>>> one or two residues with these distorted hydrogens.
>>>> Jerome
>>>> On Tuesday 21 November 2006 06:47, wrote:
>>>>> Hello,
>>>>> I want to do a simulation of a protein using NAMD and CHARMM force
>>>>> field.When I create the psf file for a protein from a pdb structure
>>>>> without hydrogens (from XR) I get a resultant structure where the
>>>>> hydrogens added (guesscoord) are very distorted (mainly the angles).
>>>>> When I minimize this structure, this distorsion does not disappear,
>>>>> but incredibly, the energy is stable after some steps. If I use this
>>>>> resultant structure for equilibration, RATTLE errors appear.
>>>>> Has anybody ever had this problem?
>>>>> Thanks a lot in advance!
>>>>> Rebeca García Fandiño
>>>>> Postdoctoral student
>>>>> Parc Cientific de Barcelona (Spain)

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