VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 15:40:05 CDT

Hi Margaret,
what parameter file are you using? The error you get (2) indicates that
you don't have parameters for some piece of what you're simulating
(likely one of the nonstandard terminii). Please let us know. You may
also want to move the discussion to NAMDL if you have further questions
about this.
Best,
Peter

Margaret Shun Cheung wrote:

>
> Dear All,
> Just a quick followup on what I tried with "auto none" as I searched
> on the web. After I included it and generated a new psf file, I got
> rid of the FATAL ERROR, but the minimization process was completely
> screwed up.
> Is there another way to get around with it? Thank you.
> Sincerely,
> Margaret
>
> On Thu, 6 Apr 2006, Margaret Shun Cheung wrote:
>
>> Dear All,
>>
>> I tried it with psfgen using the syntax in (1). But when I tried to
>> minimize the structure, namd gave me another error in (2).
>> Do I miss something in the psfgen input file? Thank you!
>> Sincerely,
>> Margaret
>>
>> (1)
>> segment A {
>> pdb my.pdb
>> first ACE
>> last CT1
>> }
>>
>>
>> (2)
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
>>
>> Charm++ fatal error:
>> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR HB CT1 HB
>>
>>
>>
>>
>>
>> On Thu, 6 Apr 2006, Margaret Shun Cheung wrote:
>>
>>>
>>> Dear All,
>>> Thank you very much for the tips!
>>> Sincerely,
>>> Margaret
>>>
>>> On Thu, 6 Apr 2006, Peter Freddolino wrote:
>>>
>>>> Dear Margaret,
>>>> you may want to look at some of the other patches that Marcos
>>>> mentioned in his email, such as ACE (acetylated N terminus) or CT1
>>>> (methylated C terminus). They are all present in the topology file.
>>>> Best,
>>>> Peter
>>>>
>>>> Margaret Shun Cheung wrote:
>>>>
>>>>> Dear John and Marcos,
>>>>>
>>>>> Thank you for the email. I looked up definitions for NTER and CTER
>>>>> and their chemical structures; this is probably not what I'd expect
>>>>> in my simulations.
>>>>> I wonder if there are options for "capped" termini, ie Acetyl and
>>>>> N-methyl options, such that charges at termini are neutral. Or is
>>>>> there another way to get around
>>>>> with charges at ends, please drop a hint.
>>>>>
>>>>> Thank you!
>>>>> Sincerely,
>>>>> Margaret
>>>>>
>>>>> On Thu, 6 Apr 2006, Marcos Sotomayor wrote:
>>>>>
>>>>>>
>>>>>> Hi Margaret,
>>>>>>
>>>>>> psfgen will build segments of your protein using a topology file
>>>>>> which defines different residues and patches. The usual CHARMM
>>>>>> topology file assumes standard protonation states for residues
>>>>>> labeled ASP (-), GLU (-), ARG (+), and LYS (+). There are three
>>>>>> options for histidine and you need to choose one of them (HSE,
>>>>>> HSD or HSP, you may want to see the first chapter of the NAMD
>>>>>> tutorial). There are several options for the termini too (charged
>>>>>> and uncharged, etc.), which can be selected through patches
>>>>>> (which can also be used to protonate ASP and GLU, see the patches
>>>>>> PRES ACP, CTER, CT1, ASPP and GLUP in the CHARMM topology file
>>>>>> provided by VMD).
>>>>>>
>>>>>> hope that helps!
>>>>>> Marcos
>>>>>>
>>>>>> On Wed, 5 Apr 2006, John Stone wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>> You'll want to read through the NAMD tutorial section
>>>>>>> about topology files, as it describes the purpose of patches
>>>>>>> for the the terminal residues:
>>>>>>> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html
>>>>>>> I don't know the answer regarding charged states, you'll have to
>>>>>>> ask
>>>>>>> Jim Phillips about that, (jim_at_ks.uiuc.edu) as he wrote the psfgen.
>>>>>>>
>>>>>>> John Stone
>>>>>>> vmd_at_ks.uiuc.edu
>>>>>>>
>>>>>>> On Tue, Apr 04, 2006 at 05:23:25PM -0400, Margaret Shun Cheung
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear VMD wizards,
>>>>>>>>
>>>>>>>> I would like to know what kind of charged states psfgen would
>>>>>>>> generate
>>>>>>>> from a standard pdb structure.
>>>>>>>> Do I have to worry about adding charges at all?
>>>>>>>> Also, when I read the psfgen user guide, it said psfgen will
>>>>>>>> patch N-terminal and C-terminal atoms. What does "patch" means?
>>>>>>>> Do these
>>>>>>>> termini carry charges?
>>>>>>>> Thank you.
>>>>>>>> Sincerely,
>>>>>>>> Margaret S. Cheung,
>>>>>>>> Ph. D. Postdoctoral Fellow,
>>>>>>>>
>>>>>>>> ------------------------------------------------------------
>>>>>>>> Room 2117 Tel: (301) 405-4892
>>>>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>>>>> ------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> NIH Resource for Macromolecular Modeling and Bioinformatics
>>>>>>> Beckman Institute for Advanced Science and Technology
>>>>>>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>>>>>> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
>>>>>>> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>>>>>>>
>>>>>>
>>>>>
>>>>> Margaret S. Cheung,
>>>>> Ph. D. Postdoctoral Fellow,
>>>>>
>>>>> ------------------------------------------------------------
>>>>> Room 2117 Tel: (301) 405-4892
>>>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>>>> University of Maryland http://glue.umd.edu/~mscheung
>>>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>>>> ------------------------------------------------------------
>>>>
>>>>
>>>
>>> Margaret S. Cheung,
>>> Ph. D. Postdoctoral Fellow,
>>>
>>> ------------------------------------------------------------
>>> Room 2117 Tel: (301) 405-4892
>>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>>> University of Maryland http://glue.umd.edu/~mscheung
>>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>>> ------------------------------------------------------------
>>>
>>
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>>
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Room 2117 Tel: (301) 405-4892
> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> University of Maryland http://glue.umd.edu/~mscheung
> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> ------------------------------------------------------------