Re: protonating ASP and GLU

From: Brian Radak (bradak_at_anl.gov)
Date: Tue Dec 13 2016 - 13:20:27 CST

There are not, to my knowledge, any recent conversions of the AMBER
force field to RTF/PRM format (I think this was last done over ten years
ago by Tom Cheatham). If you know of one, I would love to give it a try.

Brian

On 12/13/2016 01:06 PM, Giacomo Fiorin wrote:
> Hello Nehad, I believe you're better off using Leap, or in general the
> AMBER tool suite to prepare an AMBER topology. PsfGen is best suited
> for CHARMM-format force field files.
>
> Giacomo
>
> On Tue, Dec 13, 2016 at 1:48 PM, Nehad Elsalamouny <nehade_at_uow.edu.au
> <mailto:nehade_at_uow.edu.au>> wrote:
>
> I am using amber force field so what will be the modified residue
> names in that case?
>
> Nehad
>
> On Dec 14, 2016, at 1:27 AM, Brian Radak <bradak_at_anl.gov
> <mailto:bradak_at_anl.gov>> wrote:
>
>> This all depends on what force field you are using, since the
>> modified residue names are non-PDB standard as far as I know.
>>
>> For CHARMM36 the patches are ASPP and GLUP, so I would replace
>> your mutate commands with the following:
>>
>> patch GLUP xxxx:20 xxxx:25 xxxx:62
>> patch ASPP xxxx:65
>>
>> HTH,
>>
>> Brian
>>
>>
>> On 12/13/2016 05:58 AM, Nehad Elsalamouny wrote:
>>> Dear NAMD users,
>>>
>>> I need to generate a psf file with protonated ASP and GLU
>>> residues using the following script:
>>>
>>> package require psfgen
>>> topology ../../xxxx.rtf
>>> topology ../../xxxx.rtf
>>> topology ../../xxxx.rtf
>>>
>>> pdbalias atom ILE CD1 CD
>>> pdbalias residue HIS HID
>>>
>>> segment xxxx {
>>> pdb xxxx.pdb
>>> mutate 20 GLH
>>> mutate 25 GLH
>>> mutate 62A GLH
>>> mutate 65 ASH
>>> }
>>> coordpdb xxxx.pdb xxxx
>>> regenerate resids
>>> guesscoord
>>>
>>> patch DISU uPA:62 uPA:46
>>> patch DISU uPA:125 uPA:54
>>> patch DISU uPA:219 uPA:150
>>> patch DISU uPA:198 uPA:182
>>> patch DISU uPA:238 uPA:209
>>>
>>> segment xxxx {first none; last none; auto none; pub xxxx.pdb}
>>> coordpdb xxxx.pdb xxxx
>>> segment xxxx {first none; last none; auto none; pdb xxxx.pdb}
>>> coordpdb xxxx.pdb xxxx
>>> segment xxxxx {first NONE; last NONE; auto none; pdb xxxxx.pdb}
>>> coordpdb xxxxx.pdb xxxx
>>> guesscoord
>>>
>>> writepdb xxxxx.pdb
>>> writepsf xxxxx.psf
>>>
>>>
>>> The mutate command works well for for GLU and they are converted
>>> to GLH, however I receive an error message for ASP: unknown
>>> residue type ASH.
>>> What is the problem? And how can I protonate the ASP?
>>>
>>> Thanks,
>>>
>>> Nehad
>>>
>>
>> --
>> Brian Radak
>> Postdoctoral Appointee
>> Leadership Computing Facility
>> Argonne National Laboratory
>>
>> 9700 South Cass Avenue, Bldg. 240
>> Argonne, IL 60439-4854
>> (630) 252-8643 <tel:%28630%29%20252-8643>
>> brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> /"As computer programmers we have a responsibility to make sure that
> we run the computers instead of the computers running us."/ - Steve
> Oualline
>
>

-- 
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak_at_anl.gov

This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:22:43 CST