[gmx-users] Cannot find position restraint file restraint.gro

[Sailesh Bataju]

Hi,

I have been trying to simulate isobutane in urea as a solvent. I have made
myself urea.itp and urea.gro file for charmm36 forcefield under
equilibrating at certain temperature and pressure. First nvt followed by
npt I got error like this while equilibriating.

Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate
files
explicitly to avoid mistakes, although you can still use the same file as
you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Despite of this error, I continue comment define= -DPOSRE in .mdp file.
Then the simulation run smoothly without any error.

After urea has been equilibriated in  a box under certain temperature and
pressure . Now i've to put isobutane molecule in it. There has been no
error till energy minimization. But when i've to equilibriate in nvt, I got
error like this.

GROMACS:  gmx grompp, version 2018
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/sailesh/Documents/Thesis/urea_1000
Command line:
  gmx grompp -f nvt_urea.mdp -c em_urea.gro -p topol.top -o nvt_urea.tpr

Ignoring obsolete mdp entry 'title'
Generated 85052 of the 85078 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 55198 of the 85078 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Alkane_chain_A'
Excluding 3 bonded neighbours molecule type 'Urea'
Velocities were taken from a Maxwell distribution at 298 K
Removing all charge groups because cutoff-scheme=Verlet

---
Program: gmx grompp, version 2018
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)

Fatal error:
Cannot find position restraint file restraint.gro (option -r).
From GROMACS-2018, you need to specify the position restraint coordinate
files
explicitly to avoid mistakes, although you can still use the same file as
you
specify for the -c option.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---
turning all bonds into constraints...
turning all bonds into constraints...

This is my end part of topol.top file for isobutane in urea.

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include urea topology
#include "charmm36.ff/urea.itp"
#ifdef POSRES
#include "posre_urea.itp"
#endif

; Include topology for ions
#include "charmm36.ff/ions.itp"

[ system ]
; Name
Isobutane in Urea

[ molecules ]
; Compound#mols
Alkane_chain_A  2
Urea 841­

Any idea to solve this problem.

Thank you for your time and effort.

Sailesh Bataju.
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[gmx-users] MDP define in GROMACS 2018

[Joshua Mitchell]

Hi all,

I am excited to try out the new PME code in GROMACS 2018! It seems that
preprocessor variables can no longer be given values in the MDP as of
GROMACS 2018? So in 2016 I could do

define = -DPOSRES -DPOSRESFC=500.0

and then in the posres ITP:

#ifndef POSRESFC
#define POSRESFC 1000.0
#endif

[ position_restraints ]
; atom  type  fx  fy  fz
1 1  POSRESFC  POSRESFC  POSRESFC
4 1  POSRESFC  POSRESFC  POSRESFC
7 1  POSRESFC  POSRESFC  POSRESFC


And this would let me set the position restraint force constants from the
MDP, which was very convenient. I'm pretty sure I got this trick from
MARTINI so I'm not the only person who uses it. Frustratingly, in 2018 that
little equal sign causes the whole MDP define line to be ignored, causing
position restraints to fail silently. So I've spent all day trying to
figure out why it looked like my position restraints aren't working!

I think this could trick a lot of people, especially newer users trying out
MARTINI. Is the old behaviour coming back?

Oh and also, the link at http://manual.gromacs.org/documentation/ to the
2018 release notes goes to the RC-1 release notes, not the full version
release notes - seems to be missing a hyphen in the URI.

Thanks,
Josh
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[gmx-users] Is there any difference with gromacs and other MD programs?

[자연과학부]

Dear gmx users,


I’ve started to run MD simulation of ion aggregation of aqueous solution. (JCP 
145, 174501 (2016))

So I followed adding initial molecules(I gained BF4 ion topology from 
https://atb.uq.edu.au/molecule.py?molid=26889) , em, ensembles and md 
simulation. Then I calculated RDF but their g(r) values of O...O(figure 1-a in 
given journal) are slightly different between simulation on paper and I did.

My simulation reports g(0.464)=1.044.

I might guess the problem is that I used gromacs with gromos54a7 force field 
and the paper simulated with AMBER. I thought the molecules of the system is so 
simple that those force fields couldn’t be too different.


My questions are;

1. Are there any difference of calculating method between GROMACS and AMBERMD? 
If so, how can I find its details?

2. If I select AMBER force field and edit topology and run it by GROMACS, can I 
solve the simulation with completely same result with this journal?


Thank you.

Regards,

Jingyu Seol.
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Re: [gmx-users] SDS initial setup

[Dallas Warren]

A visualisation to help see what is going on with the PBC and the
molecules https://twitter.com/dr_dbw/status/909559339366572032
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 19 January 2018 at 01:03, André Farias de Moura  wrote:
> Besides the fact that there cannot be molecules outside a periodic box, are
> you sure that you want such a high SDS concentration? You are nearly 15
> times over the cmc, in the real world you would most likely end up with a
> hydrated SDS crystals (Mol. Cryst. Liq. Cryst., Vol. 549:pp. 160–165, 2011)
>
> On Thu, Jan 18, 2018 at 10:39 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 1/18/18 7:28 AM, za...@tezu.ernet.in wrote:
>>
>>> Dear Gromacs Users
>>>
>>> I am trying to simulate a protein with 200 SDS molecules.
>>>
>>> After inserting 200 molecules inside the box with the protein at the
>>> center (size of the cubic box is 324 nm3), few of the SDS molecules are
>>> outside the box from each side of the box.
>>>
>>> I have used the following command to insert the sds molecules:
>>>
>>> gmx insert-molecules -f prot.gro -ci sds.pdb -nmol 200 -o comp.gro
>>>
>>> Will it be appropriate to run simulation with this initial setup? Or do I
>>> need to make sure that entire sds molecules are inside the box.
>>>
>>
>> There is no such thing as "outside" a periodic box.
>>
>> -Justin
>>
>> --
>> ==
>>
>> 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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>>
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>>
>
>
>
> --
> _
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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[gmx-users] huge center of mass distance mismatch in umbrella sampling

[Irem Altan]

Hi,


I have two copies of a protein that are in contact with each other. Their 
center of mass distance is about 5.5 nm. However, in the resulting potential of 
mean force, there is an energetic minimum at 3.5 nm. How is this at all 
possible? At that distance half of the protein would be overlapping each other. 
How could I diagnose why this is happening?


Best,

Irem
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Re: [gmx-users] inter- and intra-molecular hbond analysis

[Mohsen Ramezanpour]

Hi Gromacs users,

I would like to know your opinion on this.

Thanks in advance for your comments

Cheers,
Mohsen

On Fri, Jan 19, 2018 at 5:16 PM, Mohsen Ramezanpour <
ramezanpour.moh...@gmail.com> wrote:

> Dear Gromacs users,
>
> Given a mixed bilayer composed of two lipids (type A and B), I would like
> to calculate:
>
> 1) "Intramolecular" h-bonds for a lipid type to see if part of lipid (NH3+
> of PE) is interacting with some other part of itself (PO4- of the same
> lipid).
>
> 2) "intermolecular" hbonds between A-A, A-B, and B-B.
>
> If I understood correctly, gmx hbond does not distinguish between the
> inter- and intra-molecular hbonds. So, choosing A and A lipids will give
> both the intramolecular and intermolecular hbonds between lipids type A in
> the system.
>
> One solution could be doing this analysis on each individual lipid of type
> A first, and then make an average over all the lipid type A in the system.
> This will give the intramolecular hbonds (lets call it H-intra)
>
> Next, calculating the hbonds between lipid A and A as gmx hbond does by
> defualt. This will give both intermolecular and intramolecular
> hbonds between A lipids in the system (Lets call it H-Both).
> Thus, (H-both) - (H-intra) = (H-intermolecular hbond between lipids of the
> same type)
>
> I think there should be an easier way to do this (especially H-intra) and
> I do not know.
> I was wondering if anyone has any suggestion?
>
> This is the same problem I am facing when I want to calculate the min-dist
> between two groups, i.e. the intermolecular and intramolecular min-distance
> between two groups of atoms.
>
> Thanks in advance for your comments,
> Cheers,
> Mohsen
>
>
>
> --
> *Rewards work better than punishment ...*
>



-- 
*Rewards work better than punishment ...*
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Re: [gmx-users] gmx dipole and gmx potential

[David van der Spoel]

Den 2018-01-21 kl. 14:27, skrev ali akgün:

Hİ all

  I am newbie and GROMACS, I did some dipole moment and electric potential
calculation for water solutions. I want to understand gmx dipole and gmx
potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not
understand about gmx dipole algorithm, so I need information about gmx
dipole algorithm.

Thank you.

Use the source... And read the papers that the program refers to, at 
least I hope it does.


--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

hi . in vmd how can i find special number for each atom? i want to delete
those atoms from my gro file.
tnx


On Mon, Jan 15, 2018 at 9:12 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 10:56 AM, negar habibzadeh wrote:
>
>> tnx so much
>>   i got nvt.tpr and now i want to run it but i am getting this error :
>> Fatal error:
>> Too many LINCS warnings (5258)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> I use position restraints on the lipid headgroups for P of DOPC . i add
>> the
>> following lines to the system topology after the #include "dopc.itp" line.
>>
>> #include "DOPC.itp"
>>
>> #ifdef POSRES_LIPID
>> #include "lipid_posre.itp"
>> #endif
>>
>> and i add the following line in nvt.mdp :
>> define  = -DPOSRES_protein  -DPOSRES_LIPID  ; Position restraint
>> for each protein and for DOPC P
>>
>> i created lipid_posre.itp :
>>
>> ; position restraint file for DOPC P
>>
>> [ position_restraints ]
>> ;  i funct   fcxfcyfcz
>> 201   0   0   1000
>> ~
>>
>> i used position restraints for lipids but again when i want to run nvt  ,i
>> get this error :
>>
>> Fatal error:
>> Too many LINCS warnings (5258)
>> If you know what you are doing you can adjust the lincs warning threshold
>> in your mdp file
>> or set the environment variable GMX_MAXCONSTRWARN to -1,
>> but normally it is better to fix the problem
>>
>> how can i solve this problem ?
>>
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
> Diagnosing_an_Unstable_System
>
> -Justin
>
>
> --
> ==
>
> 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
> /Mailing_Lists/GMX-Users_List before posting!
>
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[gmx-users] disulfide bond missing even with -ss

[ABEL Stephane]

Hi, 

If your are not sure that SS is formed or taken into account in the top file,. 
You could do a short minimization of the initial structure and observe  the 
minimized structure has the SS bond. If it also a good way to see if the top 
file is correct. 

Sté


De : gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
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Today's Topics:

   1. Re: disulfide bond missing even with -ss (MD)
   2. Re: disulfide bond missing even with -ss (Justin Lemkul)


--

Message: 1
Date: Sun, 21 Jan 2018 11:42:23 -0500
From: MD 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] disulfide bond missing even with -ss
Message-ID:

Content-Type: text/plain; charset="UTF-8"

On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 11:30 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:
>>
>>
>>> On 1/21/18 11:20 AM, MD wrote:
>>>
>>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:


 On 1/21/18 10:59 AM, MD wrote:
>
> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul 
> wrote:
>
>>
>> On 1/21/18 10:46 AM, MD wrote:
>>
>>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
>>> 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 

Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

On 1/21/18 11:42 AM, MD wrote:

On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul  wrote:



On 1/21/18 11:30 AM, MD wrote:


On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:



On 1/21/18 11:20 AM, MD wrote:

On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:


On 1/21/18 10:59 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul 
wrote:


On 1/21/18 10:46 AM, MD wrote:


On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
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.


​Yes I am very thankful for the help here and was just trying to discuss :)

The structure picture I showed is the one after pdb2gmx. I double checked
the original pdb which has disulfide bond. Then I processed the pdb with
pdb2gmx. I checked the topol_Protein_chain_B.itp and there was no disulfide
bond. I know I should stop here but I want to look at the pdb file so I
then moved forward to em.mdp and convert the em.gro to em.pdb with ​trjconv
and looked at the pdb file (the one shown in the picture), which only has
two sulfurs in close distance. The distance is about 2.0A but no disulfide
bond shown. I thought it might be chimera which didn't detect the bond but
I thought the topol_Protein_chain_B.itp or any gmx log should have
confirmed the bond formation. Does it make sense?


Yes and no.

NEVER rely on visualization software to tell you if a bond has been 
formed. They are simply guessing based on assumptions coded into them. 
The only thing that is definitive is the topology and its listing of the 
actual bonds.


Is the disulfide actually in chain B? Your screen output is incomplete 
so maybe something was lost in copy and paste and you should be looking 
in the chain A topology if it exists. There's not much more I or anyone 
can say about this because all indications are that pdb2gmx did its job 
based on (1) the lack of any error or warning and (2) the fact that Cys 
is being modeled in its oxidized form in the output coordinate file.


-Justin


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 

Re: [gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 11:33 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 11:30 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:
>>
>>
>>> On 1/21/18 11:20 AM, MD wrote:
>>>
>>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:


 On 1/21/18 10:59 AM, MD wrote:
>
> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul 
> wrote:
>
>>
>> On 1/21/18 10:46 AM, MD wrote:
>>
>>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
>>> 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.
>

​Yes I am very thankful for the help here and was just trying to discuss :)

The structure picture I showed is the one after pdb2gmx. I double checked
the original pdb which has disulfide bond. Then I processed the pdb with
pdb2gmx. I checked the topol_Protein_chain_B.itp and there was no disulfide
bond. I know I should stop here but I want to look at the pdb file so I
then moved forward to em.mdp and convert the em.gro to em.pdb with ​trjconv
and looked at the pdb file (the one shown in the picture), which only has
two sulfurs in close distance. The distance is about 2.0A but no disulfide
bond shown. I thought it might be chimera which didn't detect the bond but
I thought the topol_Protein_chain_B.itp or any gmx log should have
confirmed the bond formation. Does it make sense?

>
> 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
 

Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

On 1/21/18 11:30 AM, MD wrote:

On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:



On 1/21/18 11:20 AM, MD wrote:


On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:



On 1/21/18 10:59 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:


On 1/21/18 10:46 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
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 are0 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_

Re: [gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 11:22 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 11:20 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:
>>
>>
>>> On 1/21/18 10:59 AM, MD wrote:
>>>
>>> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:


 On 1/21/18 10:46 AM, MD wrote:
>
> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul 
> 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?​

>
>
> -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 are0 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
>> 

Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

On 1/21/18 11:20 AM, MD wrote:

On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:



On 1/21/18 10:59 AM, MD wrote:


On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:



On 1/21/18 10:46 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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.


-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 are0 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  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  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  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


--

Re: [gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 11:05 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 10:59 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:
>>
>>
>>> On 1/21/18 10:46 AM, MD wrote:
>>>
>>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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
​


>
> -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 are0 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  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  wrote:
>>>
>>> gromacs did ask me to confirm linking the two cys before the run,
>>> but I
>>>
>>> didn't see any log saying the 

Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

On 1/21/18 10:59 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:



On 1/21/18 10:46 AM, MD wrote:


On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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?


2. When you visualize the structure, both Cys335 and Cys338 are in their 
thiol (-SH) form?


-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 are0 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  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  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  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

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or

Re: [gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 10:49 AM, Justin Lemkul  wrote:

>
>
> On 1/21/18 10:46 AM, MD wrote:
>
>> On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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.​

>
>
> -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 are0 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  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  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  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
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> 

Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

On 1/21/18 10:46 AM, MD wrote:

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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?


-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 are0 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  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  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  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

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
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/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read 

Re: [gmx-users] disulfide bond missing even with -ss

[MD]

On Sun, Jan 21, 2018 at 10:37 AM, Justin Lemkul  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
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 are0 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  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  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  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
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
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Re: [gmx-users] Why gyration radius keep dropping?

[Justin Lemkul]

On 1/19/18 1:22 PM, ZHANG Cheng wrote:

Dear Gromacs,
I am running MD at 500 K for my protein.


I used this to analyse the gyration radius
echo 1 | gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg


I thought the radius should keep increase, as the protein unfolds at high 
temperature. However, all my repeats showed a dropping in the gyration radius, 
from ~2.6 nm to ~2.2 nm in 50 ns.


Can I ask if this phenomenon is common?


Proteins don't necessarily just elongate when heated. Secondary 
structure destabilizes and you are probably adopting some kind of 
non-native, molten globule. Watch the trajectory.


-Justin

--
==

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/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] -inter command

[Justin Lemkul]

On 1/20/18 2:26 AM, za...@tezu.ernet.in wrote:

Message: 1
Date: Tue, 16 Jan 2018 08:30:10 +0100
From: Jo?o Henriques 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] -inter command
Message-ID:

Re: [gmx-users] interaction force between Mg and Oxygens of phosphate, in CHARM36 force field

[Justin Lemkul]

On 1/20/18 2:42 AM, Sajad Ahrari wrote:

Hello Dears,
I am using CHARM-36.ff for my simulation. I have Mg ions and ATP as 
hetero-atoms in my system (the Mg-ATP complex). I am trying to know about the 
amount of interaction force between Mg ions and phosphates of ATP that is 
already set in this force field. Could you please help me know if I can find 
about these parameters in the force field files?


The force field files define the parameters for the different 
interactions. You can compute a LJ interaction energy using normal 
combination rules and some input distance. The same with the 
electrostatic interaction; apply Coulomb's Law. The .rtp file has the 
charges in that case, and LJ are in ffnonbonded.itp.


-Justin

--
==

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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Re: [gmx-users] disulfide bond missing even with -ss

[Justin Lemkul]

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.

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.


-Justin


On Sun, Jan 21, 2018 at 10:23 AM, MD  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  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  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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Re: [gmx-users] disulfide bond missing even with -ss

[MD]

I modified the specbond.dat and change the cutoff to be 2.04A, still
nothing...

On Sun, Jan 21, 2018 at 10:23 AM, MD  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  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  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
>>>
>>
>>
>
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Re: [gmx-users] disulfide bond missing even with -ss

[MD]

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  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  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
>>
>
>
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Re: [gmx-users] disulfide bond missing even with -ss

[MD]

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  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
>
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[gmx-users] disulfide bond missing even with -ss

[MD]

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
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[gmx-users] gmx dipole and gmx potential

[ali akgün]

Hİ all

 I am newbie and GROMACS, I did some dipole moment and electric potential
calculation for water solutions. I want to understand gmx dipole and gmx
potential algorithm.I read GROMACS manual 8.5.4 and 8.5.3 but I can not
understand about gmx dipole algorithm, so I need information about gmx
dipole algorithm.

Thank you.
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Re: [gmx-users] (no subject)

[João Henriques]

> You need some ions to neutralise the system for long range electrostatics
to work.

This mostly applies to PME. However, because PME is basically *de
facto* nowadays,
it will most likely apply in most situations. However, I recently learned
that PME can also be run with a non-neutral system, as PME will introduce a
neutralizing background charge (and dipole corrections). Here is the
thread:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg29536.html

> We usually add more to make the simulation more like the real system
(solution or cell).

Just to be the devil's advocate, I'd say that based on anecdotal evidence
adding salt in a MD simulation of a protein changes make little to no
difference. It doesn't behave as expected, most likely due to poor ion
parametrization and integer charges.

J


On Sun, Jan 21, 2018 at 7:16 AM,  wrote:

> You need some ions to neutralise the system for long range electrostatics
> to work. We usually add more to make the simulation more like the real
> system (solution or cell).
>
> > On Jan 21, 2018, at 1:12 AM, Sankaran SV . <119013...@sastra.ac.in>
> wrote:
> >
> > Dear all,
> >
> >I am a beginer. I would like to know the purpose of adding
> ions
> > during the simulation process.
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