VMD-L Mailing List

From: David Alejandro Rincón Daza (darincond_at_unal.edu.co)
Date: Wed Jun 03 2020 - 15:10:47 CDT

Hi Josh,
Thank you for your reply. I had applied your suggestions and it almost
worked
 completely.
The new results show that it passed from adding 24 new atoms to add 6 new
atoms. Punctually, psfgen added hydrogens to sulfur atoms. The error is
that those sulfur atoms belong to a disulfide bond. Thus, the sulfur atom
has ended with three bonds, one to the amino acid, two to the disulfide
bond and last one to the new bond with the new hydrogen atom. What I am
obtaining is:

*ATOM 301 HG1 CYS 22 -18.307 7.017 -9.107 0.00 0.00
 PROT ATOM 898 HG1 CYS 64 -16.442 5.402 -9.030 0.00 0.00
   PROT ATOM 3165 HG1 CYS 216 14.401 0.247 -14.391 0.00 0.00
     PROT ATOM 3286 HE2 HSP 224 3.262 2.192 2.404 0.00
 0.00 PROT ATOM 3772 HG1 CYS 258 14.360 -0.426 -15.863
 0.00 0.00 PROT ATOM 4258 HG1 CYS 293 -6.605 -6.668
 22.828 0.00 0.00 PROT ATOM 4542 HG1 CYS 311 -8.297
 -5.168 20.924 0.00 0.00 PROT *

CYS 22 is bonded by disulfide bond to CYS 64, and CYS 216 to CYS 258 and
CYS 293 to CYS 311.

   - *How can I avoid to psfgen add hydrogen atoms to sulfur atoms in
   disulfide bonds?*

Thanks in advance,
David

El mié., 3 jun. 2020 a las 11:32, Josh Vermaas (<joshua.vermaas_at_gmail.com>)
escribió:

> You will want those atoms, since they are the hydrogens attached to the
> residues. Visualize the psf/pdb pair in VMD. You'll see lots of long bonds
> to the origin for these unplaced hydrogens. What I think is going on is
> that psfgen isn't generating angles and dihedral information, so it then
> has nothing to guess atomic coordinates from. Before your
> guesscoord command, add "regenerate angles dihedrals". Then you'll find
> that psfgen will be able to guess where the atoms should go. The other
> thing you should consider is adding "first none ; last none" to the
> non-protein components, so that psfgen doesn't try adding the default NTER
> CTER patches to these residues. See below for these suggestions.
>
> -Josh
>
> *package require psfgen*
>
> *topology top_all27_prot_lipid_withSEA_TOL_TI_test2_02_link.rtf*
>
>
> *segment PROT {pdb MCC_ORI_protein.pdb}*
>
> *coordpdb MCC_ORI_protein.pdb PROT*
>
> *segment PROP {*
>
> *pdb MCC_ORI_sub.pdb*
>
> *first none*
>
> *last none*
>
> *}*
>
> *coordpdb MCC_ORI_sub.pdb PROP*
>
> *segment XWAT {pdb MCC_ORI_water.pdb}*
>
> *coordpdb MCC_ORI_water.pdb XWAT*
>
> *segment SOLV {*
>
> *pdb MCC_ORI_solvent.pdb*
>
> *first none*
>
> *last none*
>
> *}*
>
> *coordpdb MCC_ORI_solvent.pdb SOLV*
>
> *regenerate angles dihedrals*
>
>
> *guessscoord*
>
>
> *writepdb MCC_ORI_mod.pdb*
>
> *writepsf MCC_ORI_mod.psf*
>
> On Tue, Jun 2, 2020 at 4:38 PM David Alejandro Rincón Daza <
> darincond_at_unal.edu.co> wrote:
>
>> Hi, I am trying to build a PSF file. The commands that I am using are:
>>
>> in VMD -> Extension -> Tk console
>>
>> *set MCC_ORI [atomselect top protein]*
>>
>> * $MCC_ORI writepdb MCC_ORI_protein.pdb*
>>
>>
>> * set MCC_ORI [atomselect top "resname TOL"]*
>>
>> * $MCC_ORI writepdb MCC_ORI_solvent.pdb*
>>
>>
>> * set MCC_ORI [atomselect top water]*
>>
>> * $MCC_ORI writepdb MCC_ORI_water.pdb*
>>
>>
>> * set MCC_ORI [atomselect top "resname SUB"]*
>>
>> * $MCC_ORI writepdb MCC_ORI_sub.pdb*
>>
>> Then, I create a png file:
>>
>> *package require psfgen*
>>
>> * topology top_all27_prot_lipid_withSEA_TOL_TI_test2_02_link.rtf*
>>
>>
>> * segment PROT {pdb MCC_ORI_protein.pdb}*
>>
>> *coordpdb MCC_ORI_protein.pdb PROT*
>>
>> * segment PROP {pdb MCC_ORI_sub.pdb}*
>>
>> * coordpdb MCC_ORI_sub.pdb PROP*
>>
>> * segment XWAT {pdb MCC_ORI_water.pdb}*
>>
>> *coordpdb MCC_ORI_water.pdb XWAT*
>>
>> * segment SOLV {pdb MCC_ORI_solvent.pdb}*
>>
>> * coordpdb MCC_ORI_solvent.pdb SOLV*
>>
>>
>>
>> *guessscoord*
>>
>>
>> * writepdb MCC_ORI_mod.pdb*
>>
>> * writepsf MCC_ORI_mod.psf *
>>
>> and I get this info at the end of the process:
>>
>>
>>
>>
>> *psfgen) Info: guessing coordinates for 24 atoms (9 non-hydrogen)psfgen)
>> Warning: failed to guess coordinates for 17 atomspsfgen) Info: writing pdb
>> file MCC_ORI_mod_all36.pdbpsfgen) Info: Atoms with guessed coordinates will
>> have occupancy of 0.0.*
>>
>> When I do awk to the new pdb file:
>>
>> *awk '$9=="-1.00"' a*
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *ATOM 301 HG1 CYS 22 0.000 0.000 0.000 -1.00 0.00
>> PROT ATOM 898 HG1 CYS 64 0.000 0.000 0.000 -1.00 0.00
>> PROT ATOM 3165 HG1 CYS 216 0.000 0.000 0.000 -1.00 0.00
>> PROT ATOM 3286 HE2 HSP 224 0.000 0.000 0.000 -1.00
>> 0.00 PROT ATOM 3772 HG1 CYS 258 0.000 0.000 0.000
>> -1.00 0.00 PROT ATOM 4258 HG1 CYS 293 0.000 0.000
>> 0.000 -1.00 0.00 PROT ATOM 4542 HG1 CYS 311 0.000 0.000
>> 0.000 -1.00 0.00 PROT ATOM 4627 N SUB 1 0.000
>> 0.000 0.000 -1.00 0.00 PROP ATOM 4628 HT1 SUB 1 0.000
>> 0.000 0.000 -1.00 0.00 PROP ATOM 4629 HT2 SUB 1
>> 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4630 HT3 SUB 1
>> 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4631 CA SUB 1
>> 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4632 HA SUB 1
>> 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4633 C SUB
>> 1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4634 OT1 SUB
>> 1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 4635 OT2
>> SUB 1 0.000 0.000 0.000 -1.00 0.00 PROP ATOM 5528 N
>> TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM 5529
>> HT1 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM
>> 5530 HT2 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV ATOM
>> 5531 HT3 TOL 1 0.000 0.000 0.000 -1.00 0.00 SOLV
>> ATOM 5544 HA TOL 1 0.000 0.000 0.000 -1.00 0.00
>> SOLV ATOM 21808 C TOL 1086 0.000 0.000 0.000 -1.00 0.00
>> SOLV ATOM 21809 OT1 TOL 1086 0.000 0.000 0.000 -1.00 0.00
>> SOLV ATOM 21810 OT2 TOL 1086 0.000 0.000 0.000 -1.00
>> 0.00 SOLV *
>>
>> I obtain 24 atoms with the same coordinates. Moreover, this new pdb file
>> is 24 atoms larger than the original pdb.
>>
>> Questions:
>>
>> *How can I avoid that?*
>> *How can I remove them?*
>> *Is it useful to rename those atoms as DUM?*
>>
>> Looking forward
>> Thanks in advance
>>
>>
>>
>>