Re: Psfgen Errors for C-type Heme

From: Thomas Freeman (Thomas.L.Freeman_at_dartmouth.edu)
Date: Tue Mar 01 2011 - 14:15:56 CST

Thanks for the assistance Flavio, however, I do not think these topology
files will be adequate. I have used the heme topology file before with
the PHEM patch in the past but this assumes a non c-type heme. The heme
in the protein that I am working on is covalently bound to the protein
through two cys bonds and is coordinated to methionine and histidine.
This is why I have chosen to use this alternate topology file (attached).

Using the topology file you sent me along with the PHEM patch does not
produce the stray hydrogen atom but I still receive the error that the
GLU 161 O atom coordinates failed to be set.

Thanks,

-- 
Thomas Freeman
Graduate Student
Chemistry 67 Teaching Assistant
Pletneva Research Group
Department of Chemistry
Dartmouth College
On 03/01/2011 09:39 AM, flavio seixas wrote:
> Hi,
> 
> Try to use heme and protein parameters from Charmm. I attached it for you.
> Use Namd patch PHEM to bond Fe to amino acid residue His, as referenced (Seixas et al, 2008).
> 
> Regards,
> 
> Flavio
> 
> 
> --- On Mon, 2/28/11, Thomas Freeman <Thomas.L.Freeman_at_dartmouth.edu> wrote:
> 
>> From: Thomas Freeman <Thomas.L.Freeman_at_dartmouth.edu>
>> Subject: namd-l: Psfgen Errors for C-type Heme
>> To: namd-l_at_ks.uiuc.edu
>> Date: Monday, February 28, 2011, 7:46 PM
>> I am currently trying to generate a
>> pdb and psf file for a protein with
>> a c-type heme but have been getting a number of errors
>> shown below. I am
>> using the topology file for cytochrome c from: Journal of
>> Computational
>> Chemistry, 25, 1613-1622 (2004).
>>
>> ..
>> Warning: failed to set coordinate for atom
>> O     GLU:161   
>>   PROT
>> ..
>> Warning: poorly guessed coordinates for 13 atoms (2
>> non-hydrogen):
>> Warning: poorly guessed coordinate for atom
>> HT1     SER:36   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HT2     SER:36   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HT3     SER:36   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HG2     PRO:98   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HG2     PRO:102   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HG2     PRO:135   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> OT1     GLU:161   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> OT2     GLU:161   
>>   PROT
>> Warning: poorly guessed coordinate for atom
>> HA     HEMO:199   
>>   HEC
>> Warning: poorly guessed coordinate for atom
>> HB     HEMO:199   
>>   HEC
>> Warning: poorly guessed coordinate for atom
>> HC     HEMO:199   
>>   HEC
>> Warning: poorly guessed coordinate for atom
>> HD     HEMO:199   
>>   HEC
>> Warning: poorly guessed coordinate for atom
>> HBD2     HEMO:199   
>>   HEC
>> Warning: failed to guess coordinates for 1 atoms
>>
>> The psfgen input file I am using is:
>>
>> kdir -p output
>>
>> package require psfgen
>>
>> # Load topology files
>> topology toppar/top_c_heme.inp
>> topology toppar/top_all22_prot.inp
>>
>> # Generate protein segment
>> pdbalias residue HIS HSE
>> pdbalias atom ILE CD1 CD
>> segment PROT {pdb 3b42-chainA-plain.pdb}
>> coordpdb 3b42-chainA-plain.pdb PROT
>>
>> # Create segment for heme group
>> # Prevent NTER and CTER patches
>> pdbalias residue HEM HEMO
>> segment HEC {
>>     first none
>>     last none
>>     pdb 3b42-chainA-heme-plain.pdb
>> }
>> coordpdb 3b42-chainA-heme-plain.pdb HEC
>>
>> # Bind heme to protein using HOCY patch
>> patch HOCY PROT:140 PROT:143 PROT:144 PROT:60 HEC:199
>>
>> guesscoord
>>
>> # Create output files
>> writepdb output/3b42-chainA-psf-output.pdb
>> writepsf output/3b42-chainA-psf-output.psf
>>
>>
>> Opening up the pdb file that was generated shows a hydrogen
>> atom (His
>> 144 HD1) that is disconnected from the protein chain by at
>> least 10
>> angstroms.
>>
>> Any ideas for why this might be occurring and why the HD1
>> hydrogen
>> coordinates are so different from what they should be and
>> not generating
>> any sort of error?
>>
>> Thanks,
>>
>> -- 
>> Thomas Freeman
>> Graduate Student
>> Pletneva Research Group
>> Department of Chemistry
>> Dartmouth College

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