On 1/21/18 11:30 AM, MD wrote:
On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/21/18 11:20 AM, MD wrote:
On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/21/18 10:59 AM, MD wrote:
On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul <jalem...@vt.edu> wrote:
On 1/21/18 10:46 AM, MD wrote:
On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul <jalem...@vt.edu>
wrote:
On 1/21/18 10:29 AM, MD wrote:
I modified the specbond.dat and change the cutoff to be 2.04A, still
nothing...
Please don't spam the list with minute-by-minute updates.
sorry
for the scattered information,
I didn't mean to spam the thread..
Provide your pdb2gmx command, full screen output, and whatever
evidence
you have that the bond wasn't formed. The definitive answer is in your
topology. If it's not there, we can diagnose.
command line: gmx pdb2gmx -f ncat.pdb -o ncat.gro -water spc -ignh
-ss
Link CYS-335 SG-2487 and CYS-338 SG-2507 (y/n) ?y
There is no indication that anything went wrong, and this should have
been
done. Are you saying that there is no line in the topology specifying a
bond between atoms 2487 and 2507?
Right. I didn't see anything said about the bond. I went forward to
the
step of em.mdp and got a minimized gro, which was converted to pdb. And
I
found no disulfide bond in the pdb file.
So, to be clear, please answer these two questions directly:
1. You find no line in [bonds] in topol_Protein_chain_B.itp file between
atoms 2487 and 2507?
Correct.
2. When you visualize the structure, both Cys335 and Cys338 are in their
thiol (-SH) form?
T
hey are not in thiol form.
https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_
EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
This is not consistent with your above assertion. If your structure, after
pdb2gmx or any point thereafter, does not have -SH, then you are modeling a
disulfide. You can't simultaneously have no bond defined in the topology
and also have no thiols. These are mutually exclusive. I suspect the bond
was formed and you're perhaps looking in the wrong place.
Then how can we explain there are no bond formed in the
topol_Protein_chain_B.itp?
Is the image you showed before or after pdb2gmx? I'm trying to help you
figure this out, but the information at hand is not consistent unless
this structure is pre-pdb2gmx. What I was asking about was a structure
*after* processing with pdb2gmx.
If pdb2gmx has converted these Cys to -SH form despite being told
otherwise, please upload the original PDB file somewhere and provide a link.
-Justin
-Justin
-Justin
-Justin
Start terminus THR-24: NH3+
End terminus LEU-385: COO-
Opening force field file ./charmm36-jul2017.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 362 residues with 5724 atoms
Chain time...
Back Off! I just backed up topol_Protein_chain_B.itp to
./#topol_Protein_chain_B.itp.5#
Making bonds...
Warning: Long Bond (3206-3204 = 0.339276 nm)
Number of bonds was 5800, now 5800
Generating angles, dihedrals and pairs...
Before cleaning: 15256 pairs
Before cleaning: 15446 dihedrals
Keeping all generated dihedrals
Making cmap torsions...
There are 359 cmap torsion pairs
There are 15446 dihedrals, 949 impropers, 10509 angles
15142 pairs, 5800 bonds and 0 virtual sites
Total mass 40928.695 a.m.u.
Total charge -13.000 e
Writing topology
Back Off! I just backed up posre_Protein_chain_B.itp to
./#posre_Protein_chain_B.itp.5#
Processing chain 2 'B' (1 atoms, 1 residues)
Warning: Starting residue MG430 in chain not identified as
Protein/RNA/DNA.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the
behavior.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./charmm36-jul2017.ff/merged.arn
Checking for duplicate atoms....
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 1 atoms
Chain time...
Back Off! I just backed up topol_Ion_chain_B2.itp to
./#topol_Ion_chain_B2.itp.5#
Making bonds...
No bonds
Generating angles, dihedrals and pairs...
Making cmap torsions...
There are 0 dihedrals, 0 impropers, 0 angles
0 pairs, 0 bonds and 0 virtual sites
Total mass 24.305 a.m.u.
Total charge 2.000 e
Writing topology
Back Off! I just backed up posre_Ion_chain_B2.itp to
./#posre_Ion_chain_B2.itp.5#
Including chain 1 in system: 5724 atoms 362 residues
Including chain 2 in system: 1 atoms 1 residues
Now there are 5725 atoms and 363 residues
Total mass in system 40953.000 a.m.u.
Total charge in system -11.000 e
Writing coordinate file...
Back Off! I just backed up ncat.gro to ./#ncat.gro.5#
https://docs.google.com/document/d/1HOuMWAylWZOp1KP1cHRp82Y_
EiM5xAc8QM5KCAOOkSo/edit?usp=sharing
-Justin
On Sun, Jan 21, 2018 at 10:23 AM, MD <refm...@gmail.com> wrote:
I have also tried renaming my two CYS to be CYS2 but no luck either.
On Sun, Jan 21, 2018 at 10:22 AM, MD
<https://maps.google.com/?q=n,+Jan+21,+2018+at+10:22+AM,+MD&entry=gmail&source=g>
<refm...@gmail.com> wrote:
gromacs did ask me to confirm linking the two cys before the run,
but I
didn't see any log saying the bond is formed.
On Sun, Jan 21, 2018 at 10:19 AM, MD <refm...@gmail.com> wrote:
Hi Gromacs folks,
I realized I kept losing disulfide bond after gmx. The length is
2.01A
but I did use -ss when pdb2gmx. Any thoughts?
Thanks,
Ming
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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/Mailing_Lists/GMX-Users_List before posting!
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send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
--
Gromacs Users mailing list
* Please search the archive at http://www.gromacs.org/Support
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send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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