Re: [gmx-users] KALP15 in DPPC

[Justin Lemkul]

On 1/15/18 6:18 AM, negar habibzadeh wrote:

tnx Justin .
now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
your tutorial, in NVT equilibration step I created index file , with
program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
   0 System  : 30700 atoms
   1 Other   : 18744 atoms
   2 FR1 :   160 atoms
   3 FR2 :   220 atoms
   4 FR3 :   240 atoms
   5 FR4 :   205 atoms
   6 FR5 :   255 atoms
   7 DOPC: 17664 atoms
   8 CL  :40 atoms
   9 Water   : 11916 atoms
  10 SOL : 11916 atoms
  11 non-Water   : 18784 atoms
  12 Ion :40 atoms
  13 FR1 :   160 atoms
  14 FR2 :   220 atoms
  15 FR3 :   240 atoms
  16 FR4 :   205 atoms
  17 FR5 :   255 atoms
  18 DOPC: 17664 atoms
  19 CL  :40 atoms
  20 Water_and_ions  : 11956 atoms

  nr : group   !   'name' nr name   'splitch' nrEnter: list groups
  'a': atom&   'del' nr 'splitres' nr   'l': list residues
  't': atom type   |   'keep' nr'splitat' nr'h': help
  'r': residue 'res' nr 'chain' char
  "name": group'case': case sensitive   'q': save and quit
  'ri': residue index


2|3|4|5|6

Copied index group 2 'FR1'
Copied index group 3 'FR2'
Merged two groups with OR: 160 220 -> 380
Copied index group 4 'FR3'
Merged two groups with OR: 380 240 -> 620
Copied index group 5 'FR4'
Merged two groups with OR: 620 205 -> 825
Copied index group 6 'FR5'
Merged two groups with OR: 825 255 -> 1080

  21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms


name 21 protein



21|7

Copied index group 21 'protein'
Copied index group 7 'DOPC'
Merged two groups with OR: 1080 17664 -> 18744

  22 protein_DOPC: 18744 atoms


10|8

Copied index group 10 'SOL'
Copied index group 8 'CL'
Merged two groups with OR: 11916 40 -> 11956

  23 SOL_CL  : 11956 atoms


q

then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)  I'm getting this error:
Fatal error:
Group D0PC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

my nvt.mdp file is that

Can anyone help me with the following fault in Gromacs during the NVT
equilibrium?


The error specifies that you've got "D0PC" instead of "DOPC" somewhere 
in the .mdp file (note zero instead of the letter O).


-Justin



On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:



On 1/7/18 3:07 AM, negar habibzadeh wrote:


I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
your tutorial  When I use inflategro script For my System I have got
Output System_inflated.gro file with certain message in Command prompt
as follows  . The Below Message Shows That There is No Lipid Molecules
Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
Molecules Need to be Deleted ?


Maybe there just aren't any lipids overlapping with the protein; that can
happen.

-Justin


There are 128 lipids...

with 138 atoms per lipid..

Determining upper and lower leaflet...
64 lipids in the upper...
64 lipids in the lower leaflet

Centering protein
Checking for overlap
...this might actually take a while
100 % done...
There are 0 lipids within cut-off range...
0 will be removed from the upper leaflet...
0 will be removed from the lower leaflet...

Writing scaled bilayer & centered protein...


Calculating Area per lipid...
Protein X-min/max: 2441
Protein Y-min/max: 2343
X-range: 17 AY-range: 20 A
Building 17 X 20 2D grid on protein coordinates...
Calculating area occupied by protein..
full TMD..
upper TMD
lower TMD
Area per protein: 3.25 nm^2
Area per lipid: 10.7582741393 nm^2

Area per protein, upper half: 2.25 nm^2
Area per lipid, upper leaflet : 10.7738991393 nm^2

Area per protein, lower half: 2.5 nm^2
Area per lipid, lower leaflet : 10.7699928893 nm^2

Writing Area per lipid...
Done!


--
==

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] force field parameters clashing

[Justin Lemkul]

On 1/15/18 9:45 AM, Harsha Ravishankar wrote:

Dear All,

I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also obtained.

I first generate a .gro file from the pdb of the membrane using editconf.
Then I run pdb2gmx to obtain .gro and topology files of the aligned protein
molecule. I then combine the gro files of both the membrane and the protein
and create a box using editconf with the combined gro files as input.


You do not need to do any of this. CHARMM-GUI provides you with the 
coordinates of the system, a full topology, and the force field files 
necessary to carry out the simulation.


-Justin


I then edit the topology file of the protein to include the different lipid
topologies and numbers as follows,

: Include DDPC chain topology
#include "./charmm.ff/DDPC.itp"

: Include POPE chain topology
#include "./charmm.ff/POPE.itp"

: Include POPS chain topology
#include "./charmm.ff/POPS.itp"

: Include PSM chain topology
#include "./charmm.ff/PSM.itp"

: Include POPI chain topology
#include "./charmm.ff/POPI.itp

with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
are present in the membrane.

In the forcefield.itp file I specify,

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
; #include "ffnanonbonded.itp"
; #include "ffnabonded.itp"
#include "charmm_gui_membrane.itp"

The "charmm_gui_membrane.itp" file mentioned above contains the topologies
of the different lipid molecules generated by Charmm-GUI .With solvate I am
able to successfully solvate the prepared membrane-protein complex box with
SOL molecules.

However when I attempt to add ions using gmx grompp -f ions.mdp -c
solvate.gro -p topol.top -o ions.tpr, I receive a number of errors stating


"Encountered a second block of parameters for dihedral type 9 for the same
   atoms, with either different parameters and/or the first block has
multiple lines. This is not supported."

I do not quite understand why this should be the case. Any help here would
be sincerely appreciated.

Thanking everyone in advance.

Sincerely,

Harsha Ravishankar





--
==

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] KALP15 in DPPC

[negar habibzadeh]

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 ?




On Mon, Jan 15, 2018 at 6:29 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 6:18 AM, negar habibzadeh wrote:
>
>> tnx Justin .
>> now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
>>
>> your tutorial, in NVT equilibration step I created index file , with
>> program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
>>0 System  : 30700 atoms
>>1 Other   : 18744 atoms
>>2 FR1 :   160 atoms
>>3 FR2 :   220 atoms
>>4 FR3 :   240 atoms
>>5 FR4 :   205 atoms
>>6 FR5 :   255 atoms
>>7 DOPC: 17664 atoms
>>8 CL  :40 atoms
>>9 Water   : 11916 atoms
>>   10 SOL : 11916 atoms
>>   11 non-Water   : 18784 atoms
>>   12 Ion :40 atoms
>>   13 FR1 :   160 atoms
>>   14 FR2 :   220 atoms
>>   15 FR3 :   240 atoms
>>   16 FR4 :   205 atoms
>>   17 FR5 :   255 atoms
>>   18 DOPC: 17664 atoms
>>   19 CL  :40 atoms
>>   20 Water_and_ions  : 11956 atoms
>>
>>   nr : group   !   'name' nr name   'splitch' nrEnter: list groups
>>   'a': atom&   'del' nr 'splitres' nr   'l': list residues
>>   't': atom type   |   'keep' nr'splitat' nr'h': help
>>   'r': residue 'res' nr 'chain' char
>>   "name": group'case': case sensitive   'q': save and quit
>>   'ri': residue index
>>
>> 2|3|4|5|6
>>>
>> Copied index group 2 'FR1'
>> Copied index group 3 'FR2'
>> Merged two groups with OR: 160 220 -> 380
>> Copied index group 4 'FR3'
>> Merged two groups with OR: 380 240 -> 620
>> Copied index group 5 'FR4'
>> Merged two groups with OR: 620 205 -> 825
>> Copied index group 6 'FR5'
>> Merged two groups with OR: 825 255 -> 1080
>>
>>   21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms
>>
>> name 21 protein
>>>
>>
>> 21|7
>>>
>> Copied index group 21 'protein'
>> Copied index group 7 'DOPC'
>> Merged two groups with OR: 1080 17664 -> 18744
>>
>>   22 protein_DOPC: 18744 atoms
>>
>> 10|8
>>>
>> Copied index group 10 'SOL'
>> Copied index group 8 'CL'
>> Merged two groups with OR: 11916 40 -> 11956
>>
>>   23 SOL_CL  : 11956 atoms
>>
>> q
>>>
>> then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top
>> -n
>> index.ndx -o nvt.tpr)  I'm getting this error:
>> Fatal error:
>> Group D0PC referenced in the .mdp file was not found in the index file.
>> Group names must match either [moleculetype] names or custom index group
>> names, in which case you must supply an index file to the '-n' option
>> of grompp.
>>
>> my nvt.mdp file is that
>>
>> Can anyone help me with the following fault in Gromacs during the NVT
>> equilibrium?
>>
>
> The error specifies that you've got "D0PC" instead of "DOPC" somewhere in
> the .mdp file (note zero instead of the letter O).
>
> -Justin
>
>
>
>> On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/7/18 3:07 AM, negar habibzadeh wrote:
>>>
>>> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
 your tutorial  When I use inflategro script For my System I have got
 Output System_inflated.gro file with certain message in Command prompt
 as follows  . The Below Message Shows That There is No Lipid Molecules
 Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
 the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
 Molecules Need to be Deleted ?

 Maybe there just aren't any lipids overlapping with the protein; that
>>> can
>>> 

[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

[ABEL Stephane]

Hello, 

I have finally resolved my problem thank to Justin . 

Bye 
--

Message: 2
Date: Sun, 14 Jan 2018 17:36:21 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff
Message-ID: 
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 12:04 PM, ABEL Stephane wrote:
> Thank you, Justin for your interest to my problem,
>
> But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
> ILE instead of a central a simple ILE :((

Ile should not be treated as a terminal residue, and it wasn't in the
screen output you provided before after adding your custom residues to
residuetypes.dat. That's a prerequisite if you want anything to work.
Getting the connectivity right after dealing with the custom residues is
the next problem after that.

-Justin

> *gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing
>
> I will try to search a workaround
>
> Best
>
> St?phane
>
> 
> De : ABEL Stephane
> Envoy? : dimanche 14 janvier 2018 16:52
> ? : gromacs.org_gmx-users@maillist.sys.kth.se
> Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50
>
> Thanks Justin
>
> First I forgot to say that I am building a cyclic peptide (Atosiban, 
> https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
> (3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since 
> the two residues are well constructed and linked together with pdb2gmx as it 
> is shown If I consider the ILE as NILE
>
> For linking the MER and CYX I define a bond with the specbond.dat (the 
> corresponding bond is shown in the  pdb2gmx output). The only problem I have 
> is that NILE residue is chosen instead of ILE
>
> How to resolve this problem and to force pdb2gmx to use ILE ? It is strange 
> or I found a subtle error I cannot find.
>
> St?phane
>
>
>
>
> --
>
> Message: 3
> Date: Sun, 14 Jan 2018 10:34:08 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide with two
>  modified residues with amber ff
> Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 1/14/18 10:04 AM, ABEL Stephane wrote:
>> Hi Justin
>>
>> I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
>> the the following output with pdb2gmx. I select 2 and 6
>>
>> ##
>> gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
>> Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes
>>
>>
>> Select the Force Field:
>>   From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
>>1: Amber12sb ff99SB + new backbone and side chain torsion for protein
>>2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
>>3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
>>4: CHARMM36 all-atom force field (July 2017)
>>5: CHARMM36 all-atom force field, surfactants and pigments
>>6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. 
>> B 2011, 115, 487-499 )
>>7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
>> 3825?3850)
>>8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
>> Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
>>9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
>> 10.1002/jcc.21675)
>> 10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
>> 10.1007/s00249-011-0700-9)
>>   From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
>> 11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
>> 1999-2012, 2003)
>> 12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
>> 13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
>> 461-469, 1996)
>> 14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
>> 1049-1074, 2000)
>> 15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
>> 2006)
>> 16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., 
>> Proteins 78, 1950-58, 2010)
>> 17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
>> 18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
>> 19: GROMOS96 43a1 force field
>> 20: GROMOS96 43a2 force field (improved alkane dihedrals)
>> 21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>> 22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>> 23: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>> 24: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
>> 10.1007/s00249-011-0700-9)
>> 25: OPLS-AA/L all-atom force field (2001 

[gmx-users] Fwd: two very basic questions on new parameters for gromos forcefield

[Pedro Deira]

Dear all,

I have been working with some new molecules and some new bonded parameteres
that I added to the gromos 54a7 files in gromacs according to the manual
and so on, and all the results of MD simulations are in perfect agreement
with the experimental results.

However, I've just been reviewing this odd paper and I'm stuck with these
very very basic questions that make me question if I'm working as I should:

- When we select a gromos force field, or derivative, it will use, for
example, the force constants provided in the definition files for that ff,
and those are written in agreement with table 5.5 of the manual, say, bond
force constant comes in kJ mol-1 nm-4, right ?

- Therefore, when we compute the force constant values, we should use the
equation from the corresponding force field, right? For example, for
gromos96 fourth power potential (page 74 of 2018 manual), the value we
include in the ff parameters if the k_ij^b in equation 4.35, and not any
other value, right?

Thanks for any comments,
All the best,
pd
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[gmx-users] force field parameters clashing

[Harsha Ravishankar]

Dear All,

I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also obtained.

I first generate a .gro file from the pdb of the membrane using editconf.
Then I run pdb2gmx to obtain .gro and topology files of the aligned protein
molecule. I then combine the gro files of both the membrane and the protein
and create a box using editconf with the combined gro files as input.

I then edit the topology file of the protein to include the different lipid
topologies and numbers as follows,

: Include DDPC chain topology
#include "./charmm.ff/DDPC.itp"

: Include POPE chain topology
#include "./charmm.ff/POPE.itp"

: Include POPS chain topology
#include "./charmm.ff/POPS.itp"

: Include PSM chain topology
#include "./charmm.ff/PSM.itp"

: Include POPI chain topology
#include "./charmm.ff/POPI.itp

with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
are present in the membrane.

In the forcefield.itp file I specify,

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
; #include "ffnanonbonded.itp"
; #include "ffnabonded.itp"
#include "charmm_gui_membrane.itp"

The "charmm_gui_membrane.itp" file mentioned above contains the topologies
of the different lipid molecules generated by Charmm-GUI .With solvate I am
able to successfully solvate the prepared membrane-protein complex box with
SOL molecules.

However when I attempt to add ions using gmx grompp -f ions.mdp -c
solvate.gro -p topol.top -o ions.tpr, I receive a number of errors stating


"Encountered a second block of parameters for dihedral type 9 for the same
  atoms, with either different parameters and/or the first block has
multiple lines. This is not supported."

I do not quite understand why this should be the case. Any help here would
be sincerely appreciated.

Thanking everyone in advance.

Sincerely,

Harsha Ravishankar



-- 
Harsha Ravishankar
harsha.ravishan...@scilifelab.se
Doctoral candidate in Biophysics
Theoretical and Computational Biophysics
KTH - Science for Life Laboratory, Stockholm
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[gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

Hi Gromacs folks,

I have a modified amino acid which has all the parameters set. However, the
last error is the "cmap torsion between atoms xxx" and it would't go
away. Basically the cmap contains atoms of  C-N-CA-C-N from three residues,
where the CA is my newly modified residue. THe only thing I could think of
is the newly modified residue was not recognized by gromacs, but I have
checked the residue.dat, the log from pdb2gmx and it looks like this
residue was not considered "alien". Got stuck here any help will be
appreciated!

Best,

Ming
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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[Justin Lemkul]

On 1/15/18 2:56 PM, MD wrote:

updated, I figured it is because my N and CA have different type names than
charmm, which is weird cause I used CHARMM GUI to get the itp files for the
modified amino acid. Would it be an easy fix if I manually change those two
atom names or I should go a different route for the cmap problem?


CHARMM-GUI can only parametrize a species via the interface to CGenFF. 
This is not appropriate for integral residues in a polypeptide chain. 
The backbone of each amino acid is the same; yours has different atom 
types (presumably from CGenFF) that are not the same as the normal 
types. This makes the application of CMAP parameters impossible.


You should separately parametrize your side chain using CHARMM atom 
types; the initial charges provided by CGenFF can be used as a first 
guess but should be subject to refinement as needed. A proper 
parametrization protocol will involve vibrational analysis, dipole 
moment analysis, water interactions, and conformational energy scans. It 
is laborious but if you want a custom residue to be consistent with the 
highly optimized protein force field, you have to do the work.


-Justin


Thanks,

Ming

On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:


Hi Gromacs folks,

I have a modified amino acid which has all the parameters set. However,
the last error is the "cmap torsion between atoms xxx" and it would't
go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
residues, where the CA is my newly modified residue. THe only thing I could
think of is the newly modified residue was not recognized by gromacs, but I
have checked the residue.dat, the log from pdb2gmx and it looks like this
residue was not considered "alien". Got stuck here any help will be
appreciated!

Best,

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] why does gromacs want to draw a cmap covering my new inserted residue?

[Justin Lemkul]

On 1/15/18 3:06 PM, MD wrote:

I wonder if there is a way I can create my own cmap for those modified type
names and incorporate the cmap to the cmap.itp?


That will end up being far more work than a proper parametrization of 
the side chain while leaving the backbone alone at standard atom types 
and charges.


-Justin


Thanks,
Ming

On Mon, Jan 15, 2018 at 2:56 PM, MD  wrote:


updated, I figured it is because my N and CA have different type names
than charmm, which is weird cause I used CHARMM GUI to get the itp files
for the modified amino acid. Would it be an easy fix if I manually change
those two atom names or I should go a different route for the cmap problem?

Thanks,

Ming

On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:


Hi Gromacs folks,

I have a modified amino acid which has all the parameters set. However,
the last error is the "cmap torsion between atoms xxx" and it would't
go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
residues, where the CA is my newly modified residue. THe only thing I could
think of is the newly modified residue was not recognized by gromacs, but I
have checked the residue.dat, the log from pdb2gmx and it looks like this
residue was not considered "alien". Got stuck here any help will be
appreciated!

Best,

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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[gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

[ABEL Stephane]

>> Would you be willing to share the exact sequence of events, commands, etc. 
>> that worked?

OK, 

Consider that the Atosiban cyclic peptide 
(https://fr.wikipedia.org/wiki/Atosiban) with 2 custom residues 
(3-Mercaptopropionyl, MEr) and ethyloxyde TYR (TYO) at Nter. The Mer is bonded 
to the CYS with SS bond and to TYO. Since we have no hdb for  for these 
residues. I first added manually the Hs in MEr and TYO with pymol with their 
corresponding names listed in the rtp (myAtosiban.pdb). 

My "problem" was to linked the Mer and TYO  and TYO with ILE by two peptide 
bonds and thus form a SS bond with Mer and CYS

1) consider the Mer and TYO as Protein residues and add  in residuetypes.dat 
the following lines

 MER Protein
 TYO Protein
 
 2) construct the corresponding rtp for these two custom residues (the RESP 
charges were derived with PyRED) Disclaimer ; these charges are "absolutely 
not" tested 
 
  TYO rtp 
  ; RESP partial charges derived from PyRED
  ; residue has similar structure than TYR
[ TYO ]
 [ atoms ]
 NN-0.5197 1
 HH 0.2770 2
CACX0.4385 3
HAH10.0423 4
CBCT   -0.1978 5
   HB1HC0.0698 6
   HB2HC0.0698 7
CGCA0.0563 8
   CD1CA   -0.2130 9
   HD1HA0.141710
   CE1CA   -0.162711
   HE1HA0.137312
   CZ C 0.271413
   OE OS   -0.384414
   C2 CT0.171515
   H21H10.031316
   H22H10.031317
   C3 CT   -0.052618
   H31HC0.019419
   H32HC0.019420
   H33HC0.019421
   CD2CA   -0.213022
   HD2HA0.141723
   CE2CA   -0.162724
   HE2HA0.137325
C C 0.404726 ; CO in PyRED
O O-0.574227

[ bonds ]
 N H
 NCA
CAHA
CACB
CA C
CB   HB1
CB   HB2
CBCG
CG   CD1
CG   CD2
   CD1   HD1
   CD1   CE1
   CE1   HE1
   CE1CZ
CZOE
OEC2
C2H21
C2H22
C2C3
C3H31
C3H32
C3H33
CZCE2
   CE2   HE2
   CE2   CD2
   CD2   HD2
 C O
 C+N  ---> here the trick to make a peptide bond with ILE

 [ impropers ]
-CCA N H
CA+N C O
CG   CE2   CD2   HD2
CZ   CD2   CE2   HE2
   CD1CZ   CE1   HE1
CG   CE1   CD1   HD1
   CD1   CD2CGCB
   CE1   CE2CZOE
   
 MER 
 
 ; Mercapto
;
;  S1
;   |
;  H21-C2-H22
;   |
;   H31-C3-H32
;   |
;   C=O

; RESP partial charges derived from PyRED

[ MER ]
 [ atoms ]
S1  S -0.1994  1
C2  CT 0.0424  2   ; same as C3 in PyRED
H21 H1 0.0631  3   ; same as H31 in PyRED
H22 H1 0.0631  4   ; same as H32 in PyRED
C3  CT-0.0157  5   ; same as C4 in PyRED
H31 H1 0.0295  6   ; same as H41 in PyRED
H32 H1 0.0295  7   ; same as H42 in PyRED
C   C  0.5373  8   ; same as C2 in PyRED
O   O -0.5498  9   ; same as O1 in PyRED

[ bonds ]
 S1   C2
 C2   H21
 C2   H22
 C2   C3
 C3   H31
 C3   H32
 C3   C
 CO
 C   +N  --> here the trick to make a peptide bond with TYO

 [ impropers ]
C3+N C O

3) to make a SS bond between Mer and CYS. Add in the specbondat the following 
line 

1
MER S1  1   CYX SG  1   0.20380 MER  CYX  ;; S-S 
bond distance in Amber

And to finish use the following command to construct the top file 

mpirun -np 1 gmx_mpi pdb2gmx -f myAtosiban.pdb -p myAtosiban.top -o 
myAtosiban_H.pdb -i myAtosiban_posre.itp -missing -rtpres

and perform a short minimization to check if the three bonds are correctly set 
(not broken). 

Stéphane 

--

Message: 2
Date: Mon, 15 Jan 2018 12:42:16 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
modified residues with amber ff -- Resolved
Message-ID: 
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/15/18 12:31 PM, ABEL Stephane wrote:
> Hello,
>
> I have finally resolved my problem thank to Justin .

Would you be willing to share the exact sequence of events, commands,
etc. that worked? As I mentioned before, these threads often trail off
or end unresolved, so while it is nice that you solved your own problem,
it would be beneficial to the community to document how you did it so
that others might learn.

-Justin

> Bye
> --
>
> Message: 2
> Date: Sun, 14 Jan 2018 17:36:21 -0500
> From: Justin Lemkul 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Problem fpr building a peptide with two
>  modified residues with amber ff
> Message-ID: 

[gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[ZHANG Cheng]

Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue. For example, a buried big residue may have similar sasa as an exposed 
small residue.


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] Problem fpr building a peptide with two modified residues with amber ff -- Resolved

[Justin Lemkul]

On 1/15/18 12:31 PM, ABEL Stephane wrote:

Hello,

I have finally resolved my problem thank to Justin .


Would you be willing to share the exact sequence of events, commands, 
etc. that worked? As I mentioned before, these threads often trail off 
or end unresolved, so while it is nice that you solved your own problem, 
it would be beneficial to the community to document how you did it so 
that others might learn.


-Justin


Bye
--

Message: 2
Date: Sun, 14 Jan 2018 17:36:21 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
 modified residues with amber ff
Message-ID: 
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 12:04 PM, ABEL Stephane wrote:

Thank you, Justin for your interest to my problem,

But even if I use the -missing argument*, pdb2gmx still wants to add an Nter 
ILE instead of a central a simple ILE :((

Ile should not be treated as a terminal residue, and it wasn't in the
screen output you provided before after adding your custom residues to
residuetypes.dat. That's a prerequisite if you want anything to work.
Getting the connectivity right after dealing with the custom residues is
the next problem after that.

-Justin


*gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -missing

I will try to search a workaround

Best

St?phane


De : ABEL Stephane
Envoy? : dimanche 14 janvier 2018 16:52
? : gromacs.org_gmx-users@maillist.sys.kth.se
Objet : RE:gromacs.org_gmx-users Digest, Vol 165, Issue 50

Thanks Justin

First I forgot to say that I am building a cyclic peptide (Atosiban, 
https://fr.wikipedia.org/wiki/Atosiban). I construct two RTP for the  MER 
(3-Mercaptopropionyl-) and TYO (ethoxy tyrosine. And they are correct since the 
two residues are well constructed and linked together with pdb2gmx as it is 
shown If I consider the ILE as NILE

For linking the MER and CYX I define a bond with the specbond.dat (the 
corresponding bond is shown in the  pdb2gmx output). The only problem I have is 
that NILE residue is chosen instead of ILE

How to resolve this problem and to force pdb2gmx to use ILE ? It is strange or 
I found a subtle error I cannot find.

St?phane




--

Message: 3
Date: Sun, 14 Jan 2018 10:34:08 -0500
From: Justin Lemkul 
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem fpr building a peptide with two
  modified residues with amber ff
Message-ID: <541ddbd0-378e-16eb-79a4-f161235d4...@vt.edu>
Content-Type: text/plain; charset=utf-8; format=flowed



On 1/14/18 10:04 AM, ABEL Stephane wrote:

Hi Justin

I have added the TYO and MER residue as Protein is the residuetypes.dat. And 
the the following output with pdb2gmx. I select 2 and 6

##
 gmx_mpi pdb2gmx -f Atosiban_box_ctr.pdb -p Atosiban_amber14sb.top -o 
Atosiban_amber14sb.pdb -i Atosiban_posre.itp -rtpres yes


Select the Force Field:
   From '/ccc/work/cont003/dsv/abel01/ForceFields/GMX_ForceFields/top/':
1: Amber12sb ff99SB + new backbone and side chain torsion for protein
2: AMBER14SB_parmbsc1 (ff14SB for protein + parmbsc1 for DNA)
3: AMBER94 BCL force field (J. Comp. Chem. 2012, 33, 1969?1980)
4: CHARMM36 all-atom force field (July 2017)
5: CHARMM36 all-atom force field, surfactants and pigments
6: GLYCAM06 force field for alkylglycosides and RG1 (2011, J. Phys. Chem. B 
2011, 115, 487-499 )
7: GROMOS96 2016H66 force field (J. Chem. Theory. Comput., 2016, 12, 
3825?3850)
8: GROMOS96 53a6 force field with PVP (JCC 2004 vol 25 pag 1656 and J. 
Phys. Chem. C, 2015, 119 (14), pp 7888?7899)
9: GROMOS96 53a6carbo force field (JCC 2011 vol 32 pag 998, doi 
10.1002/jcc.21675)
10: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40,, 843-856, DOI: 
10.1007/s00249-011-0700-9)
   From '/ccc/products/gromacs-5.1.2/default/share/gromacs/top':
11: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 
1999-2012, 2003)
12: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
13: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 
461-469, 1996)
14: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 
1049-1074, 2000)
15: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 
2006)
16: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 
78, 1950-58, 2010)
17: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
18: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
19: GROMOS96 43a1 force field
20: GROMOS96 43a2 force field (improved alkane dihedrals)
21: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
22: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
23: GROMOS96 53a6 force field (JCC 2004 vol 

Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

updated, I figured it is because my N and CA have different type names than
charmm, which is weird cause I used CHARMM GUI to get the itp files for the
modified amino acid. Would it be an easy fix if I manually change those two
atom names or I should go a different route for the cmap problem?

Thanks,

Ming

On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:

> Hi Gromacs folks,
>
> I have a modified amino acid which has all the parameters set. However,
> the last error is the "cmap torsion between atoms xxx" and it would't
> go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
> residues, where the CA is my newly modified residue. THe only thing I could
> think of is the newly modified residue was not recognized by gromacs, but I
> have checked the residue.dat, the log from pdb2gmx and it looks like this
> residue was not considered "alien". Got stuck here any help will be
> appreciated!
>
> Best,
>
> Ming
>
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Re: [gmx-users] Fwd: two very basic questions on new parameters for gromos forcefield

[Justin Lemkul]

On 1/15/18 9:57 AM, Pedro Deira wrote:

Dear all,

I have been working with some new molecules and some new bonded parameteres
that I added to the gromos 54a7 files in gromacs according to the manual
and so on, and all the results of MD simulations are in perfect agreement
with the experimental results.

However, I've just been reviewing this odd paper and I'm stuck with these
very very basic questions that make me question if I'm working as I should:

- When we select a gromos force field, or derivative, it will use, for
example, the force constants provided in the definition files for that ff,
and those are written in agreement with table 5.5 of the manual, say, bond
force constant comes in kJ mol-1 nm-4, right ?


Yes.


- Therefore, when we compute the force constant values, we should use the
equation from the corresponding force field, right? For example, for
gromos96 fourth power potential (page 74 of 2018 manual), the value we
include in the ff parameters if the k_ij^b in equation 4.35, and not any
other value, right?


Yes.

-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] KALP15 in DPPC

[Justin Lemkul]

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

==

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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[Justin Lemkul]

On 1/15/18 3:52 PM, ZHANG Cheng wrote:

Thank you! So if I am using a index file, and the index 1 is the group I am interested, should I 
use the below? What is the difference between "-output" and "-o"?


-output is the group you select for output, -o is the file to which the 
data are written. Please read gmx help sasa if you're not clear what the 
options are doing.




echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns


The command requires two selections, one for the surface, the other for 
what is output. See 
http://manual.gromacs.org/documentation/2018-latest/user-guide/cmdline.html#g-sas


-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] force field parameters clashing

[Justin Lemkul]

On 1/15/18 1:27 PM, Harsha Ravishankar wrote:

Hello Justin,

Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating Couldn't
find topology match for atomtype NP.

I am not sure as to what is the source of such errors.


CHARMM-GUI will only provide a topology and subset of the force field 
that is pertinent to the system you provide it. If you subsequently add 
things into the mix, it won't account for necessary parameters. If 
you're going to take this approach, use CHARMM-GUI to build the entire 
system.


-Justin


best wishes

Harsha



On Mon, Jan 15, 2018 at 3:58 PM, Justin Lemkul  wrote:



On 1/15/18 9:45 AM, Harsha Ravishankar wrote:


Dear All,

I am a beginner with Gromacs and simulations and I want to simulate a
membrane and protein complex with the membrane comprising of 5 different
lipid molecules. The membrane was generated with Charmm-GUI and the
appropriate Gromacs parameters for the different lipids were also
obtained.

I first generate a .gro file from the pdb of the membrane using editconf.
Then I run pdb2gmx to obtain .gro and topology files of the aligned
protein
molecule. I then combine the gro files of both the membrane and the
protein
and create a box using editconf with the combined gro files as input.


You do not need to do any of this. CHARMM-GUI provides you with the
coordinates of the system, a full topology, and the force field files
necessary to carry out the simulation.

-Justin


I then edit the topology file of the protein to include the different lipid

topologies and numbers as follows,

: Include DDPC chain topology
#include "./charmm.ff/DDPC.itp"

: Include POPE chain topology
#include "./charmm.ff/POPE.itp"

: Include POPS chain topology
#include "./charmm.ff/POPS.itp"

: Include PSM chain topology
#include "./charmm.ff/PSM.itp"

: Include POPI chain topology
#include "./charmm.ff/POPI.itp

with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
are present in the membrane.

In the forcefield.itp file I specify,

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
; #include "ffnanonbonded.itp"
; #include "ffnabonded.itp"
#include "charmm_gui_membrane.itp"

The "charmm_gui_membrane.itp" file mentioned above contains the topologies
of the different lipid molecules generated by Charmm-GUI .With solvate I
am
able to successfully solvate the prepared membrane-protein complex box
with
SOL molecules.

However when I attempt to add ions using gmx grompp -f ions.mdp -c
solvate.gro -p topol.top -o ions.tpr, I receive a number of errors stating


"Encountered a second block of parameters for dihedral type 9 for the same
atoms, with either different parameters and/or the first block has
multiple lines. This is not supported."

I do not quite understand why this should be the case. Any help here would
be sincerely appreciated.

Thanking everyone in advance.

Sincerely,

Harsha Ravishankar





--
==

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
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Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[Justin Lemkul]

On 1/15/18 1:50 PM, ZHANG Cheng wrote:

Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like the 
"absolute" sasa, as it could not reflect the relative exposure extent of a residue. For 
example, a buried big residue may have similar sasa as an exposed small residue.


Yes, if you select the full surface as the calculation group and the 
residue(s) of interest as the output group, you can easily calculate the 
relative contribution to the surface.


-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] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

Thank you so much for the guide Justin! The path looks clearer to me now :)
Ming

On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 2:56 PM, MD wrote:
>
>> updated, I figured it is because my N and CA have different type names
>> than
>> charmm, which is weird cause I used CHARMM GUI to get the itp files for
>> the
>> modified amino acid. Would it be an easy fix if I manually change those
>> two
>> atom names or I should go a different route for the cmap problem?
>>
>
> CHARMM-GUI can only parametrize a species via the interface to CGenFF.
> This is not appropriate for integral residues in a polypeptide chain. The
> backbone of each amino acid is the same; yours has different atom types
> (presumably from CGenFF) that are not the same as the normal types. This
> makes the application of CMAP parameters impossible.
>
> You should separately parametrize your side chain using CHARMM atom types;
> the initial charges provided by CGenFF can be used as a first guess but
> should be subject to refinement as needed. A proper parametrization
> protocol will involve vibrational analysis, dipole moment analysis, water
> interactions, and conformational energy scans. It is laborious but if you
> want a custom residue to be consistent with the highly optimized protein
> force field, you have to do the work.
>
> -Justin
>
> Thanks,
>>
>> Ming
>>
>> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>>
>> Hi Gromacs folks,
>>>
>>> I have a modified amino acid which has all the parameters set. However,
>>> the last error is the "cmap torsion between atoms xxx" and it would't
>>> go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
>>> residues, where the CA is my newly modified residue. THe only thing I
>>> could
>>> think of is the newly modified residue was not recognized by gromacs,
>>> but I
>>> have checked the residue.dat, the log from pdb2gmx and it looks like this
>>> residue was not considered "alien". Got stuck here any help will be
>>> appreciated!
>>>
>>> Best,
>>>
>>> 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] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

I wonder if there is a way I can create my own cmap for those modified type
names and incorporate the cmap to the cmap.itp?
Thanks,
Ming

On Mon, Jan 15, 2018 at 2:56 PM, MD  wrote:

> updated, I figured it is because my N and CA have different type names
> than charmm, which is weird cause I used CHARMM GUI to get the itp files
> for the modified amino acid. Would it be an easy fix if I manually change
> those two atom names or I should go a different route for the cmap problem?
>
> Thanks,
>
> Ming
>
> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>
>> Hi Gromacs folks,
>>
>> I have a modified amino acid which has all the parameters set. However,
>> the last error is the "cmap torsion between atoms xxx" and it would't
>> go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
>> residues, where the CA is my newly modified residue. THe only thing I could
>> think of is the newly modified residue was not recognized by gromacs, but I
>> have checked the residue.dat, the log from pdb2gmx and it looks like this
>> residue was not considered "alien". Got stuck here any help will be
>> appreciated!
>>
>> Best,
>>
>> Ming
>>
>
>
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[gmx-users] Uncorrelated Samples, MBAR free energy calculations.

[Javad Noroozi]

Dear All,


I am getting very low number of uncorrelated samples at endpoint of 
electrostatics transformation.

Anyone is familiar with MBAR pyhton script?


Javad
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Re: [gmx-users] Can I get the fraction of solvent accessible surface area using "gmx sasa"?

[ZHANG Cheng]

Thank you! So if I am using a index file, and the index 1 is the group I am 
interested, should I use the below? What is the difference between "-output" 
and "-o"?


echo 1|gmx sasa -f md_0_1.xtc -s md_0_1.tpr -surface -output -n -o area.xvg -tu 
ns




-- Original --
From:  "ZHANG Cheng";<272699...@qq.com>;
Date:  Tue, Jan 16, 2018 02:50 AM
To:  "gromacs.org_gmx-users";

Subject:  Can I get the fraction of solvent accessible surface area using "gmx 
sasa"?



Dear Gromacs,
This website can give us the Q(SASA), i.e. the fraction of SASA per residue, 
with values from 0 to 1.
https://mathbio.crick.ac.uk/wiki/POPS


Can I ask if we can use "gmx sasa" to obtain similar information? I do not like 
the "absolute" sasa, as it could not reflect the relative exposure extent of a 
residue. For example, a buried big residue may have similar sasa as an exposed 
small residue.


Thank you.


Yours sincerely
Cheng
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Re: [gmx-users] force field parameters clashing

[Harsha Ravishankar]

Hello Justin,

Thanks for the reply. I only make use of Charmm GUI to generate the
membrane patch, as I need to orient my protein in a particular orientation.
However when I made use of the .itp forcefield files in gmx grompp -f
ions.mdp -c solvate.gro -p topol.top -o ions.tpr I get errors stating Couldn't
find topology match for atomtype NP.

I am not sure as to what is the source of such errors.

best wishes

Harsha



On Mon, Jan 15, 2018 at 3:58 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 9:45 AM, Harsha Ravishankar wrote:
>
>> Dear All,
>>
>> I am a beginner with Gromacs and simulations and I want to simulate a
>> membrane and protein complex with the membrane comprising of 5 different
>> lipid molecules. The membrane was generated with Charmm-GUI and the
>> appropriate Gromacs parameters for the different lipids were also
>> obtained.
>>
>> I first generate a .gro file from the pdb of the membrane using editconf.
>> Then I run pdb2gmx to obtain .gro and topology files of the aligned
>> protein
>> molecule. I then combine the gro files of both the membrane and the
>> protein
>> and create a box using editconf with the combined gro files as input.
>>
>
> You do not need to do any of this. CHARMM-GUI provides you with the
> coordinates of the system, a full topology, and the force field files
> necessary to carry out the simulation.
>
> -Justin
>
>
> I then edit the topology file of the protein to include the different lipid
>> topologies and numbers as follows,
>>
>> : Include DDPC chain topology
>> #include "./charmm.ff/DDPC.itp"
>>
>> : Include POPE chain topology
>> #include "./charmm.ff/POPE.itp"
>>
>> : Include POPS chain topology
>> #include "./charmm.ff/POPS.itp"
>>
>> : Include PSM chain topology
>> #include "./charmm.ff/PSM.itp"
>>
>> : Include POPI chain topology
>> #include "./charmm.ff/POPI.itp
>>
>> with DDPC, POPE, POPS, PSM, POPI being the different lipid molecules that
>> are present in the membrane.
>>
>> In the forcefield.itp file I specify,
>>
>> #include "ffnonbonded.itp"
>> #include "ffbonded.itp"
>> #include "gb.itp"
>> #include "cmap.itp"
>> ; Nucleic acids nonbonded and bonded parameters"
>> ; #include "ffnanonbonded.itp"
>> ; #include "ffnabonded.itp"
>> #include "charmm_gui_membrane.itp"
>>
>> The "charmm_gui_membrane.itp" file mentioned above contains the topologies
>> of the different lipid molecules generated by Charmm-GUI .With solvate I
>> am
>> able to successfully solvate the prepared membrane-protein complex box
>> with
>> SOL molecules.
>>
>> However when I attempt to add ions using gmx grompp -f ions.mdp -c
>> solvate.gro -p topol.top -o ions.tpr, I receive a number of errors stating
>>
>>
>> "Encountered a second block of parameters for dihedral type 9 for the same
>>atoms, with either different parameters and/or the first block has
>> multiple lines. This is not supported."
>>
>> I do not quite understand why this should be the case. Any help here would
>> be sincerely appreciated.
>>
>> Thanking everyone in advance.
>>
>> Sincerely,
>>
>> Harsha Ravishankar
>>
>>
>>
>>
> --
> ==
>
> 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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>



-- 
Harsha Ravishankar
harsha.ravishan...@scilifelab.se
Doctoral candidate in Biophysics
Theoretical and Computational Biophysics
KTH - Science for Life Laboratory, Stockholm
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Re: [gmx-users] -inter command

[João Henriques]

A lot of OPs have the tendency to follow-up with private emails and I feel
it should stay public so other people might benefit from the information as
well. Here is the rest of the conversation regarding this thread.

"""
Dear Zaved,

I'm not aware of any tutorials for Gromacs, and Gromacs does not support
constant-pH MD simulations straight out of the box. It must be (heavily)
modified. Amber comes pre-packaged with constant-pH functionality, I
believe. Still, you probably don't want to get involved in any of this. My
comment about it was merely to make you aware that changing the protonation
states by hand doesn't make mean you're really simulating at a given pH.
Still, 99.9% of the people in this field do what you were wanting to do,
i.e., change the protonation states during pdb2gmx to whatever they feel is
more representative of that residue at a given pH and then hit run. I also
do it, unless I'm studying something where charge regulation playes a major
role, so by all means go ahead and try the simpler solution first.

P.S.: Please avoid sending private messages about these subjects. It
started in gmx-users and should stay there for several reasons. The main
one is that other people might have the same problem and this information
might be useful for them as well.

Best regards,
J

On Tue, Jan 16, 2018 at 6:54 AM,  wrote:

> Dear Sir
>
> Thank you for your kind response regarding the -inter command.
>
> Sir can you guide / provide any tutorial for constant-pH MD simulation in
> gromacs (eg., to perform simulation at pH 9)?
>
> I shall be grateful to you for the same.
>
> Thank You
>
> Regards
> Zaved Hazarika
> Research Scholar
> C/O Dr. A.N. Jha
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> Napam, 784028,
> Assam,
> India
>
>
> * * * D I S C L A I M E R * * *
> This e-mail may contain privileged information and is intended solely for
> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.

"""

J

On Mon, Jan 15, 2018 at 11:51 AM, João Henriques <
joao.m.a.henriq...@gmail.com> wrote:

> -inter sets the interactive mode for a bunch of other flags. Most are used
> for selecting the protonation states of the termini and other residues. It
> can also be used for interactive SS bridge selection.
>
> > "for setting the protonation state of charged amino acids in order to
> perform simulation at different pH?"
>
> Please note that changing the protonation states of the residues does not
> mean you're performing the simulation at a "different pH". A proper
> constant-pH MD simulation allows the residues to titrate in respect to the
> solution pH as well as the their "molecular environment". In this case,
> your residues will be "stuck" in a user defined protonation state that may
> or may not reflect the most populated protonation states of those residues
> at a given pH, irrespectively of their surroundings.
>
> Cheers,
> J
>
> On Mon, Jan 15, 2018 at 11:00 AM,  wrote:
>
>> Dear Gromacs Users
>>
>> I have an query regarding gmx pdb2gmx -inter command.
>>
>> Do we use -inter command only for setting the protonation state of charged
>> amino acids in order to perform simulation at different pH?
>>
>>
>> Thank You
>>
>> Regards
>> Zaved Hazarika
>> Research Scholar
>> Dept. Of Molecular Biology and Biotechnology,
>> Tezpur University,
>> India
>>
>>
>> * * * D I S C L A I M E R * * *
>> This e-mail may contain privileged information and is intended solely for
>> the individual named. If you are not the named addressee you should not
>> disseminate, distribute or copy this e-mail. Please notify the sender
>> immediately by e-mail if you have received this e-mail in error and destroy
>> it from your system. Though considerable effort has been made to deliver
>> error free e-mail messages but it can not be guaranteed to be secure or
>> error-free as information could be intercepted, corrupted, lost, destroyed,
>> delayed, or may contain viruses. The recipient must verify the integrity of
>> this e-mail message.
>> --
>> 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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>>
>
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[gmx-users] Rupture force definition

[Rakesh Mishra]

Dear, all

I have one  query regarding pulling of si-rNA (having chain-a and chain-b).
Here, I am pulling 3' end of chain-a and fixed 3' end of chain-b
(diagonally apposite ). I am doing pulling using gromacs with constant
velocity rate using Umbrella sampling. after finalization of pulling before
umbrella sampling, we got two output file i.e.

1- force/time (f= force)
2- x/time (x= pulling distance between two ends)

in first case of f/t, initially force increases and then after some  time,
force starts
to decrease (looks like gaussian curve, not exactly gaussian, because lot
of fluctuation). So my question is that, what this peak (of increasing and
decreasing curve ) represents. can I define this peak as a rupture force or
breaking force of two strands of si-rna or something else.



-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +91877749632*
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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

I mean it is disconnected after energy minimization, i found out the CO is
not connecting with the NH from the +1 amino acid. The structure was intact
before the simulation.

Ming

On Mon, Jan 15, 2018 at 6:23 PM, MD  wrote:

> Hi another quick question, what do you think could be the problem if the
> modified amino acid is not connecting to the +1 amino acid? the [cmap ] in
> merged.rtp already has the [ cmap ]-C NCA C+N
>
> Ming
>
> On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:
>
>>
>>
>> On 1/15/18 2:56 PM, MD wrote:
>>
>>> updated, I figured it is because my N and CA have different type names
>>> than
>>> charmm, which is weird cause I used CHARMM GUI to get the itp files for
>>> the
>>> modified amino acid. Would it be an easy fix if I manually change those
>>> two
>>> atom names or I should go a different route for the cmap problem?
>>>
>>
>> CHARMM-GUI can only parametrize a species via the interface to CGenFF.
>> This is not appropriate for integral residues in a polypeptide chain. The
>> backbone of each amino acid is the same; yours has different atom types
>> (presumably from CGenFF) that are not the same as the normal types. This
>> makes the application of CMAP parameters impossible.
>>
>> You should separately parametrize your side chain using CHARMM atom
>> types; the initial charges provided by CGenFF can be used as a first guess
>> but should be subject to refinement as needed. A proper parametrization
>> protocol will involve vibrational analysis, dipole moment analysis, water
>> interactions, and conformational energy scans. It is laborious but if you
>> want a custom residue to be consistent with the highly optimized protein
>> force field, you have to do the work.
>>
>> -Justin
>>
>> Thanks,
>>>
>>> Ming
>>>
>>> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>>>
>>> Hi Gromacs folks,

 I have a modified amino acid which has all the parameters set. However,
 the last error is the "cmap torsion between atoms xxx" and it
 would't
 go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
 residues, where the CA is my newly modified residue. THe only thing I
 could
 think of is the newly modified residue was not recognized by gromacs,
 but I
 have checked the residue.dat, the log from pdb2gmx and it looks like
 this
 residue was not considered "alien". Got stuck here any help will be
 appreciated!

 Best,

 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.
>>
>
>
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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

Hi another quick question, what do you think could be the problem if the
modified amino acid is not connecting to the +1 amino acid? the [cmap ] in
merged.rtp already has the [ cmap ]-C NCA C+N

Ming

On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 2:56 PM, MD wrote:
>
>> updated, I figured it is because my N and CA have different type names
>> than
>> charmm, which is weird cause I used CHARMM GUI to get the itp files for
>> the
>> modified amino acid. Would it be an easy fix if I manually change those
>> two
>> atom names or I should go a different route for the cmap problem?
>>
>
> CHARMM-GUI can only parametrize a species via the interface to CGenFF.
> This is not appropriate for integral residues in a polypeptide chain. The
> backbone of each amino acid is the same; yours has different atom types
> (presumably from CGenFF) that are not the same as the normal types. This
> makes the application of CMAP parameters impossible.
>
> You should separately parametrize your side chain using CHARMM atom types;
> the initial charges provided by CGenFF can be used as a first guess but
> should be subject to refinement as needed. A proper parametrization
> protocol will involve vibrational analysis, dipole moment analysis, water
> interactions, and conformational energy scans. It is laborious but if you
> want a custom residue to be consistent with the highly optimized protein
> force field, you have to do the work.
>
> -Justin
>
> Thanks,
>>
>> Ming
>>
>> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>>
>> Hi Gromacs folks,
>>>
>>> I have a modified amino acid which has all the parameters set. However,
>>> the last error is the "cmap torsion between atoms xxx" and it would't
>>> go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
>>> residues, where the CA is my newly modified residue. THe only thing I
>>> could
>>> think of is the newly modified residue was not recognized by gromacs,
>>> but I
>>> have checked the residue.dat, the log from pdb2gmx and it looks like this
>>> residue was not considered "alien". Got stuck here any help will be
>>> appreciated!
>>>
>>> Best,
>>>
>>> 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
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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[Justin Lemkul]

On 1/15/18 6:25 PM, MD wrote:

I mean it is disconnected after energy minimization, i found out the CO is
not connecting with the NH from the +1 amino acid. The structure was intact
before the simulation.


That has nothing to do with CMAP, that means you didn't properly define 
a bond to the +1 residue.


-Justin


Ming

On Mon, Jan 15, 2018 at 6:23 PM, MD  wrote:


Hi another quick question, what do you think could be the problem if the
modified amino acid is not connecting to the +1 amino acid? the [cmap ] in
merged.rtp already has the [ cmap ]-C NCA C+N

Ming

On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:



On 1/15/18 2:56 PM, MD wrote:


updated, I figured it is because my N and CA have different type names
than
charmm, which is weird cause I used CHARMM GUI to get the itp files for
the
modified amino acid. Would it be an easy fix if I manually change those
two
atom names or I should go a different route for the cmap problem?


CHARMM-GUI can only parametrize a species via the interface to CGenFF.
This is not appropriate for integral residues in a polypeptide chain. The
backbone of each amino acid is the same; yours has different atom types
(presumably from CGenFF) that are not the same as the normal types. This
makes the application of CMAP parameters impossible.

You should separately parametrize your side chain using CHARMM atom
types; the initial charges provided by CGenFF can be used as a first guess
but should be subject to refinement as needed. A proper parametrization
protocol will involve vibrational analysis, dipole moment analysis, water
interactions, and conformational energy scans. It is laborious but if you
want a custom residue to be consistent with the highly optimized protein
force field, you have to do the work.

-Justin

Thanks,

Ming

On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:

Hi Gromacs folks,

I have a modified amino acid which has all the parameters set. However,
the last error is the "cmap torsion between atoms xxx" and it
would't
go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
residues, where the CA is my newly modified residue. THe only thing I
could
think of is the newly modified residue was not recognized by gromacs,
but I
have checked the residue.dat, the log from pdb2gmx and it looks like
this
residue was not considered "alien". Got stuck here any help will be
appreciated!

Best,

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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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

Sorry I didn't mean to connect it to the cmap. Yes it is a different
question. How do I define a bond to the +1 residue please? It is a side
chain modified amino acid (LYS) and the backbone is unchanged. What else do
I need to take care to make sure the backbone still connects?

Thanks a bunch,

Ming

On Mon, Jan 15, 2018 at 6:26 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 6:25 PM, MD wrote:
>
>> I mean it is disconnected after energy minimization, i found out the CO is
>> not connecting with the NH from the +1 amino acid. The structure was
>> intact
>> before the simulation.
>>
>
> That has nothing to do with CMAP, that means you didn't properly define a
> bond to the +1 residue.
>
> -Justin
>
>
> Ming
>>
>> On Mon, Jan 15, 2018 at 6:23 PM, MD  wrote:
>>
>> Hi another quick question, what do you think could be the problem if the
>>> modified amino acid is not connecting to the +1 amino acid? the [cmap ]
>>> in
>>> merged.rtp already has the [ cmap ]-C NCA C+N
>>>
>>> Ming
>>>
>>> On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:
>>>
>>>
 On 1/15/18 2:56 PM, MD wrote:

 updated, I figured it is because my N and CA have different type names
> than
> charmm, which is weird cause I used CHARMM GUI to get the itp files for
> the
> modified amino acid. Would it be an easy fix if I manually change those
> two
> atom names or I should go a different route for the cmap problem?
>
> CHARMM-GUI can only parametrize a species via the interface to CGenFF.
 This is not appropriate for integral residues in a polypeptide chain.
 The
 backbone of each amino acid is the same; yours has different atom types
 (presumably from CGenFF) that are not the same as the normal types. This
 makes the application of CMAP parameters impossible.

 You should separately parametrize your side chain using CHARMM atom
 types; the initial charges provided by CGenFF can be used as a first
 guess
 but should be subject to refinement as needed. A proper parametrization
 protocol will involve vibrational analysis, dipole moment analysis,
 water
 interactions, and conformational energy scans. It is laborious but if
 you
 want a custom residue to be consistent with the highly optimized protein
 force field, you have to do the work.

 -Justin

 Thanks,

> Ming
>
> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>
> Hi Gromacs folks,
>
>> I have a modified amino acid which has all the parameters set.
>> However,
>> the last error is the "cmap torsion between atoms xxx" and it
>> would't
>> go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
>> residues, where the CA is my newly modified residue. THe only thing I
>> could
>> think of is the newly modified residue was not recognized by gromacs,
>> but I
>> have checked the residue.dat, the log from pdb2gmx and it looks like
>> this
>> residue was not considered "alien". Got stuck here any help will be
>> appreciated!
>>
>> Best,
>>
>> 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

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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
> /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.
>
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Re: [gmx-users] why does gromacs want to draw a cmap covering my new inserted residue?

[Justin Lemkul]

On 1/15/18 6:36 PM, MD wrote:

Sorry I didn't mean to connect it to the cmap. Yes it is a different
question. How do I define a bond to the +1 residue please? It is a side
chain modified amino acid (LYS) and the backbone is unchanged. What else do
I need to take care to make sure the backbone still connects?


You need a bond between C and +N (see any other amino acid in the .rtp 
file to check your work).


-Justin


Thanks a bunch,

Ming

On Mon, Jan 15, 2018 at 6:26 PM, Justin Lemkul  wrote:



On 1/15/18 6:25 PM, MD wrote:


I mean it is disconnected after energy minimization, i found out the CO is
not connecting with the NH from the +1 amino acid. The structure was
intact
before the simulation.


That has nothing to do with CMAP, that means you didn't properly define a
bond to the +1 residue.

-Justin


Ming

On Mon, Jan 15, 2018 at 6:23 PM, MD  wrote:

Hi another quick question, what do you think could be the problem if the

modified amino acid is not connecting to the +1 amino acid? the [cmap ]
in
merged.rtp already has the [ cmap ]-C NCA C+N

Ming

On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul  wrote:



On 1/15/18 2:56 PM, MD wrote:

updated, I figured it is because my N and CA have different type names

than
charmm, which is weird cause I used CHARMM GUI to get the itp files for
the
modified amino acid. Would it be an easy fix if I manually change those
two
atom names or I should go a different route for the cmap problem?

CHARMM-GUI can only parametrize a species via the interface to CGenFF.

This is not appropriate for integral residues in a polypeptide chain.
The
backbone of each amino acid is the same; yours has different atom types
(presumably from CGenFF) that are not the same as the normal types. This
makes the application of CMAP parameters impossible.

You should separately parametrize your side chain using CHARMM atom
types; the initial charges provided by CGenFF can be used as a first
guess
but should be subject to refinement as needed. A proper parametrization
protocol will involve vibrational analysis, dipole moment analysis,
water
interactions, and conformational energy scans. It is laborious but if
you
want a custom residue to be consistent with the highly optimized protein
force field, you have to do the work.

-Justin

Thanks,


Ming

On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:

Hi Gromacs folks,


I have a modified amino acid which has all the parameters set.
However,
the last error is the "cmap torsion between atoms xxx" and it
would't
go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
residues, where the CA is my newly modified residue. THe only thing I
could
think of is the newly modified residue was not recognized by gromacs,
but I
have checked the residue.dat, the log from pdb2gmx and it looks like
this
residue was not considered "alien". Got stuck here any help will be
appreciated!

Best,

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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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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--
==

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] why does gromacs want to draw a cmap covering my new inserted residue?

[MD]

whooops, never paid attention to the C N+, my bad, thank you Justin :)
Ming

On Mon, Jan 15, 2018 at 6:39 PM, Justin Lemkul  wrote:

>
>
> On 1/15/18 6:36 PM, MD wrote:
>
>> Sorry I didn't mean to connect it to the cmap. Yes it is a different
>> question. How do I define a bond to the +1 residue please? It is a side
>> chain modified amino acid (LYS) and the backbone is unchanged. What else
>> do
>> I need to take care to make sure the backbone still connects?
>>
>
> You need a bond between C and +N (see any other amino acid in the .rtp
> file to check your work).
>
> -Justin
>
>
> Thanks a bunch,
>>
>> Ming
>>
>> On Mon, Jan 15, 2018 at 6:26 PM, Justin Lemkul  wrote:
>>
>>
>>> On 1/15/18 6:25 PM, MD wrote:
>>>
>>> I mean it is disconnected after energy minimization, i found out the CO
 is
 not connecting with the NH from the +1 amino acid. The structure was
 intact
 before the simulation.

 That has nothing to do with CMAP, that means you didn't properly define
>>> a
>>> bond to the +1 residue.
>>>
>>> -Justin
>>>
>>>
>>> Ming
>>>
 On Mon, Jan 15, 2018 at 6:23 PM, MD  wrote:

 Hi another quick question, what do you think could be the problem if the

> modified amino acid is not connecting to the +1 amino acid? the [cmap ]
> in
> merged.rtp already has the [ cmap ]-C NCA C+N
>
> Ming
>
> On Mon, Jan 15, 2018 at 3:09 PM, Justin Lemkul 
> wrote:
>
>
> On 1/15/18 2:56 PM, MD wrote:
>>
>> updated, I figured it is because my N and CA have different type names
>>
>>> than
>>> charmm, which is weird cause I used CHARMM GUI to get the itp files
>>> for
>>> the
>>> modified amino acid. Would it be an easy fix if I manually change
>>> those
>>> two
>>> atom names or I should go a different route for the cmap problem?
>>>
>>> CHARMM-GUI can only parametrize a species via the interface to
>>> CGenFF.
>>>
>> This is not appropriate for integral residues in a polypeptide chain.
>> The
>> backbone of each amino acid is the same; yours has different atom
>> types
>> (presumably from CGenFF) that are not the same as the normal types.
>> This
>> makes the application of CMAP parameters impossible.
>>
>> You should separately parametrize your side chain using CHARMM atom
>> types; the initial charges provided by CGenFF can be used as a first
>> guess
>> but should be subject to refinement as needed. A proper
>> parametrization
>> protocol will involve vibrational analysis, dipole moment analysis,
>> water
>> interactions, and conformational energy scans. It is laborious but if
>> you
>> want a custom residue to be consistent with the highly optimized
>> protein
>> force field, you have to do the work.
>>
>> -Justin
>>
>> Thanks,
>>
>> Ming
>>>
>>> On Mon, Jan 15, 2018 at 1:34 PM, MD  wrote:
>>>
>>> Hi Gromacs folks,
>>>
>>> I have a modified amino acid which has all the parameters set.
 However,
 the last error is the "cmap torsion between atoms xxx" and it
 would't
 go away. Basically the cmap contains atoms of  C-N-CA-C-N from three
 residues, where the CA is my newly modified residue. THe only thing
 I
 could
 think of is the newly modified residue was not recognized by
 gromacs,
 but I
 have checked the residue.dat, the log from pdb2gmx and it looks like
 this
 residue was not considered "alien". Got stuck here any help will be
 appreciated!

 Best,

 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
>>>

[gmx-users] six member ring won't stay flat

[MD]

Hi Gromacs,

I have a modified side chain amino acid and it has a six member ring
attached to it. Regarding this ring I had dihedral angles taken care with
some 0s and some 180s. However, after minimization my structure looks very
strange, the ring is not flat and the dihedral angles in my settings didn't
seem to apply to the minimized structure at all. Any thoughts?

Thanks,

Ming
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Re: [gmx-users] six member ring won't stay flat

[Justin Lemkul]

On 1/15/18 7:45 PM, MD wrote:

Hi Gromacs,

I have a modified side chain amino acid and it has a six member ring
attached to it. Regarding this ring I had dihedral angles taken care with
some 0s and some 180s. However, after minimization my structure looks very
strange, the ring is not flat and the dihedral angles in my settings didn't
seem to apply to the minimized structure at all. Any thoughts?


You're going to have to provide a lot more detail. You're parametrizing 
something nonstandard, so there are plenty of places to make mistakes. 
Without knowing your structure, the actual parameters and how derived 
and validated them, there's nothing to do but guess.


Keep in mind that rings are not necessarily perfectly planar, and the 
values set for dihedral phase offsets do not strictly mean the values 
that the dihedrals must adopt.


-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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[gmx-users] rlist

[Faezeh Pousaneh]

Hi,

I have a user-potential for vdw and coulomb (PME-user). I use vdW and
columnb cutoffs= 0.3 and 0.5 respectively. What should be the value of
rlist?

sorry, I could not find in manual.

Best regards
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[gmx-users] gaff

[mmahmoudig]

hi i want draw topology file for ligand with gaff force field, does
gromacs can run this force field?
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[gmx-users] Info on umbrella sampling simulation

[Matteo Busato]

Dear all,


I'm performing an umbrella sampling simulation on an ion pulled from the bulk 
of a phase1 to the COM of a phase2 (taken as reference) along the z-axys in a 
biphasic system to calculate the PMF related to the transfer from phase1 to 
phase2. The box is 3.62 X 3.62 X 7.24 nm and the interphase is more or less at 
z = 3.62 nm. This is the pulling part of the .mdp file for the pulling 
simulation:


; Pull code
pull= umbrella
pull-ngroups= 2
pull-group1_name= Other
pull-group2_name= zn
pull-geometry= distance
pull-coord1-groups  = 1 2
pull-ncoords = 1
pull-dim = N N Y
pull-coord1-rate= -0.02
pull-coord1-k   = 1000
pull-start   = yes


36 configurations have been chosen to cover a path from the bulk of phase1 
(distance with COM of phase2 = 3.4 nm) to the COM of phase2. Each configuration 
was equilibrated for 5 ns and then simulated for 10 ns in NPT conditions 
(298.15 K, 1 atm). This is the pulling part of the .mdp file for the NPT 
simulation of each configuration:


; Pull code
pull= umbrella
pull-ngroups= 2
pull-group1_name= Other
pull-group2_name= zn
pull-geometry= distance
pull-coord1-groups  = 1 2
pull-ncoords = 1
pull-dim = N N Y
pull-coord1-rate= 0.0
pull-coord1-k   = 5000
pull-start   = yes
refcoord_scaling = com


In addition to the umbrella potential, position restraints of 2000 KJ mol-1 
nm-2 on the x and y-axes have been applied to the ion to prevent movement on 
the xy-plane.


This is the obtained PMF profile:

https://ibb.co/hj9je6


and these are the histograms:

https://ibb.co/cYssXR


I was wandering:


1) why the PMF curve doesn't reach a plateau when the ion is in the middle of 
the phase1, i.e. for d close to zero. Could it depend on the simulation time or 
should I build a bigger box so that the ion is sorrounded by a larger amount of 
phase1?


2) why I get those little jumps on the plateau from d = 2.5 nm to d = 3.4 nm 
(ion close to the middle of phase 1). The histograms seem to be quite well 
overlapped.


Thank you in advance for your answers


Kind regards,

Matteo Busato
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Re: [gmx-users] KALP15 in DPPC

[negar habibzadeh]

tnx Justin .
now I am doing  Simulation of *5 *Peptide in DOPC Lipids  I am following
your tutorial, in NVT equilibration step I created index file , with
program make_ndx (gmx make_ndx -f em.gro -o index.ndx) :
  0 System  : 30700 atoms
  1 Other   : 18744 atoms
  2 FR1 :   160 atoms
  3 FR2 :   220 atoms
  4 FR3 :   240 atoms
  5 FR4 :   205 atoms
  6 FR5 :   255 atoms
  7 DOPC: 17664 atoms
  8 CL  :40 atoms
  9 Water   : 11916 atoms
 10 SOL : 11916 atoms
 11 non-Water   : 18784 atoms
 12 Ion :40 atoms
 13 FR1 :   160 atoms
 14 FR2 :   220 atoms
 15 FR3 :   240 atoms
 16 FR4 :   205 atoms
 17 FR5 :   255 atoms
 18 DOPC: 17664 atoms
 19 CL  :40 atoms
 20 Water_and_ions  : 11956 atoms

 nr : group   !   'name' nr name   'splitch' nrEnter: list groups
 'a': atom&   'del' nr 'splitres' nr   'l': list residues
 't': atom type   |   'keep' nr'splitat' nr'h': help
 'r': residue 'res' nr 'chain' char
 "name": group'case': case sensitive   'q': save and quit
 'ri': residue index

> 2|3|4|5|6

Copied index group 2 'FR1'
Copied index group 3 'FR2'
Merged two groups with OR: 160 220 -> 380
Copied index group 4 'FR3'
Merged two groups with OR: 380 240 -> 620
Copied index group 5 'FR4'
Merged two groups with OR: 620 205 -> 825
Copied index group 6 'FR5'
Merged two groups with OR: 825 255 -> 1080

 21 FR1_FR2_FR3_FR4_FR5 :  1080 atoms

> name 21 protein


> 21|7

Copied index group 21 'protein'
Copied index group 7 'DOPC'
Merged two groups with OR: 1080 17664 -> 18744

 22 protein_DOPC: 18744 atoms

> 10|8

Copied index group 10 'SOL'
Copied index group 8 'CL'
Merged two groups with OR: 11916 40 -> 11956

 23 SOL_CL  : 11956 atoms

> q

then ... when i run grommp (gmx grompp -f nvt.mdp -c em.gro -p topol.top -n
index.ndx -o nvt.tpr)  I'm getting this error:
Fatal error:
Group D0PC referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.

my nvt.mdp file is that

Can anyone help me with the following fault in Gromacs during the NVT
equilibrium?


On Tue, Jan 9, 2018 at 4:31 PM, Justin Lemkul  wrote:

>
>
> On 1/7/18 3:07 AM, negar habibzadeh wrote:
>
>> I am doing  Simulation of *γ-AA*Peptide in DOPC Lipids  I am following
>> your tutorial  When I use inflategro script For my System I have got
>> Output System_inflated.gro file with certain message in Command prompt
>> as follows  . The Below Message Shows That There is No Lipid Molecules
>> Are Deleted  Should I Change the Cut-off or scaling Factor  to Delete
>> the Lipid Molecules or is it enough ,  I Mean  Must Some Lipid
>> Molecules Need to be Deleted ?
>>
>
> Maybe there just aren't any lipids overlapping with the protein; that can
> happen.
>
> -Justin
>
>
> There are 128 lipids...
>> with 138 atoms per lipid..
>>
>> Determining upper and lower leaflet...
>> 64 lipids in the upper...
>> 64 lipids in the lower leaflet
>>
>> Centering protein
>> Checking for overlap
>> ...this might actually take a while
>> 100 % done...
>> There are 0 lipids within cut-off range...
>> 0 will be removed from the upper leaflet...
>> 0 will be removed from the lower leaflet...
>>
>> Writing scaled bilayer & centered protein...
>>
>>
>> Calculating Area per lipid...
>> Protein X-min/max: 2441
>> Protein Y-min/max: 2343
>> X-range: 17 AY-range: 20 A
>> Building 17 X 20 2D grid on protein coordinates...
>> Calculating area occupied by protein..
>> full TMD..
>> upper TMD
>> lower TMD
>> Area per protein: 3.25 nm^2
>> Area per lipid: 10.7582741393 nm^2
>>
>> Area per protein, upper half: 2.25 nm^2
>> Area per lipid, upper leaflet : 10.7738991393 nm^2
>>
>> Area per protein, lower half: 2.5 nm^2
>> Area per lipid, lower leaflet : 10.7699928893 nm^2
>>
>> Writing Area per lipid...
>> Done!
>>
>
> --
> ==
>
> 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] Error while compiling GROMACS 2018

[Paul Bauer]

Hello,

it seems like you have some manually copied files in your source tree. 
Please try to remove them and build again.
The line you see in the first error message was changed during the 
recent testing (listed-forces/bonded.cpp) and is causing the error in 
your local copy (listed-forces/bonded_2.cpp).


Cheers

Paul

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[gmx-users] -inter command

[zaved]

Dear Gromacs Users

I have an query regarding gmx pdb2gmx -inter command.

Do we use -inter command only for setting the protonation state of charged
amino acids in order to perform simulation at different pH?


Thank You

Regards
Zaved Hazarika
Research Scholar
Dept. Of Molecular Biology and Biotechnology,
Tezpur University,
India


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Re: [gmx-users] -inter command

[João Henriques]

-inter sets the interactive mode for a bunch of other flags. Most are used
for selecting the protonation states of the termini and other residues. It
can also be used for interactive SS bridge selection.

> "for setting the protonation state of charged amino acids in order to
perform simulation at different pH?"

Please note that changing the protonation states of the residues does not
mean you're performing the simulation at a "different pH". A proper
constant-pH MD simulation allows the residues to titrate in respect to the
solution pH as well as the their "molecular environment". In this case,
your residues will be "stuck" in a user defined protonation state that may
or may not reflect the most populated protonation states of those residues
at a given pH, irrespectively of their surroundings.

Cheers,
J

On Mon, Jan 15, 2018 at 11:00 AM,  wrote:

> Dear Gromacs Users
>
> I have an query regarding gmx pdb2gmx -inter command.
>
> Do we use -inter command only for setting the protonation state of charged
> amino acids in order to perform simulation at different pH?
>
>
> Thank You
>
> Regards
> Zaved Hazarika
> Research Scholar
> Dept. Of Molecular Biology and Biotechnology,
> Tezpur University,
> India
>
>
> * * * D I S C L A I M E R * * *
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> the individual named. If you are not the named addressee you should not
> disseminate, distribute or copy this e-mail. Please notify the sender
> immediately by e-mail if you have received this e-mail in error and destroy
> it from your system. Though considerable effort has been made to deliver
> error free e-mail messages but it can not be guaranteed to be secure or
> error-free as information could be intercepted, corrupted, lost, destroyed,
> delayed, or may contain viruses. The recipient must verify the integrity of
> this e-mail message.
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