date:20141117

Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-17 Thread soumadwip ghosh

Dear Justin,
   thanks for your reply. I really dont know how to create
the .itp file from the .pdb file of the TMA cation. Do I need a topology
builder? After making the .itp file, how should I proceed? If I have to add
it by genion, then I guess the tma.itp must be a part of the ions.itp file
of the forcefield directory, right?
Please elaborate.

Regards,
Soumadwip
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[gmx-users] (no subject)

2014-11-17 Thread soumadwip ghosh

Dear Justin,
   thanks for your reply. I really dont know how to create
the .itp file from the .pdb file of the TMA cation. Do I need a topology
builder? After making the .itp file, how should I proceed? If I have to add
it by genion, then I guess the tma.itp must be a part of the ions.itp file
of the forcefield directory, right?
Please elaborate.

Regards,
Soumadwip
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[gmx-users] Umbrella Sampling gromacs 5.0 error

2014-11-17 Thread Alexander Law

Dear vmx-users

I am running through Dr Lemkul's umbrella sampling tutorial and applying this 
to my own structure. I have problem with the pull simulation command: grompp -f 
md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr

I receive this error message back:


Ignoring obsolete mdp entry 'title'

Ignoring obsolete mdp entry 'optimize_fft'

Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'

ERROR: pull-coord1-groups should have 2 components


WARNING 1 [file md_pull.mdp, line 62]:

  Unknown left-hand 'pull-group0' in parameter file




WARNING 2 [file md_pull.mdp, line 62]:

  Unknown left-hand 'pull-group1' in parameter file




WARNING 3 [file md_pull.mdp, line 62]:

  Unknown left-hand 'pull_rate1' in parameter file




WARNING 4 [file md_pull.mdp, line 62]:

  Unknown left-hand 'pull_k1' in parameter file




NOTE 2 [file md_pull.mdp]:

  With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note

  that with the Verlet scheme, nstlist has no effect on the accuracy of

  your simulation.



NOTE 3 [file md_pull.mdp]:

  nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting

  nstcomm to nstcalcenergy



NOTE 4 [file md_pull.mdp]:

  leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1


--

Fatal error:

Group Protein 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 Index file is set up properly, with force being applied to Chain_A, and 
Chain_B is my static reference:

0 Chain_B :  1290 atoms

1 Chain_A :   110 atoms


The md_pull.mdp remains the same:


; Pull code

pull= umbrella

pull_geometry   = distance  ; simple distance increase

pull_dim= N N Y

pull_start  = yes   ; define initial COM distance > 0

pull_ngroups= 1

pull_group0 = Chain_B

pull_group1 = Chain_A

pull_rate1  = 0.01  ; 0.01 nm per ps = 10 nm per ns

pull_k1 = 1000  ; kJ mol^-1 nm^-2


Any advice on how to treat this problem is appreciated.


Cheers,

Alex


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Re: [gmx-users] problem with phosphorylated serine

2014-11-17 Thread Justin Lemkul




On 11/17/14 6:55 PM, Jayant James wrote:

Hi!
Thanks it did work after I added "SEPProtein" to the residuetypes.dat
file. While executing pdb2gmx I found that I am asked to choose the water
model and I choose SPC. Then I got the error that stating that (Error
message below).

Error Message
-
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2gmx.c, line: 1879
Fatal error:
The topology file 'gromos43a1p.ff/spc.itp' for the selected water model
'spc' can not be found in the force field directory. Select a different
water model.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Hence I went and listed the files in the non-phosphorylate and
phosphorylated directories and found that many files in the
non-phosphorylated directory are *not *present in the phosphorylated
directory (given below)

$ ls gromos43a1.ff/
aminoacids.c.tdb  *aminoacids.vsd  * forcefield.doc   *spce.itp*
aminoacids.hdbatomtypes.atpforcefield.itp   *spc.itp*
aminoacids.n.tdb  ffbonded.itp *ions.itp tip3p.itp*
aminoacids.r2b*ff_dum.itp   methanol216.gro*  *tip4p.itp*
aminoacids.rtpffnonbonded.itp  *methanol216.gro*  watermodels.dat

$ ls gromos43a1p.ff/
aminoacids.c.tdb  aminoacids.rtp   forcefield.doc  watermodels.dat
aminoacids.hdbatomtypes.atpforcefield.itp
aminoacids.n.tdb  ffbonded.itp MD5SUM.txt
aminoacids.r2bffnonbonded.itp  README

SO MY QUESTION IS: Is it ok to copy these files that are missing in the
phosphorylated force field directory from the non-phosphorylated
force field directory?



Yes.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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Re: [gmx-users] problem with phosphorylated serine

2014-11-17 Thread Jayant James

Hi!
Thanks it did work after I added "SEPProtein" to the residuetypes.dat
file. While executing pdb2gmx I found that I am asked to choose the water
model and I choose SPC. Then I got the error that stating that (Error
message below).

Error Message
-
Program pdb2gmx, VERSION 4.5.4
Source code file: pdb2gmx.c, line: 1879
Fatal error:
The topology file 'gromos43a1p.ff/spc.itp' for the selected water model
'spc' can not be found in the force field directory. Select a different
water model.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
---


Hence I went and listed the files in the non-phosphorylate and
phosphorylated directories and found that many files in the
non-phosphorylated directory are *not *present in the phosphorylated
directory (given below)

$ ls gromos43a1.ff/
aminoacids.c.tdb  *aminoacids.vsd  * forcefield.doc   *spce.itp*
aminoacids.hdbatomtypes.atpforcefield.itp   *spc.itp*
aminoacids.n.tdb  ffbonded.itp *ions.itp tip3p.itp*
aminoacids.r2b*ff_dum.itp   methanol216.gro*  *tip4p.itp*
aminoacids.rtpffnonbonded.itp  *methanol216.gro*  watermodels.dat

$ ls gromos43a1p.ff/
aminoacids.c.tdb  aminoacids.rtp   forcefield.doc  watermodels.dat
aminoacids.hdbatomtypes.atpforcefield.itp
aminoacids.n.tdb  ffbonded.itp MD5SUM.txt
aminoacids.r2bffnonbonded.itp  README

SO MY QUESTION IS: Is it ok to copy these files that are missing in the
phosphorylated force field directory from the non-phosphorylated
force field directory?

Thank you
JJ


On Mon, Nov 17, 2014 at 11:40 AM, Justin Lemkul  wrote:

>
>
> On 11/17/14 1:25 PM, Jayant James wrote:
>
>> Hi!
>> I had actually downloaded the *gromos43a1p-4.5.1.tgz (47 KB) file, *it
>> was not the ffG43a1p.tar.gz as said earlier. Sorry about the
>> miscommunication.
>> So *gromos43a1p-4.5.1.tgz *file was unpacked and placed in
>>
>> /share/apps/gromacs/4.5.4/single/share/gromacs/top/ and it creates the
>> gromos43a1p.ff directory. Under the directory are the files
>>
>> aminoacids.c.tdb  aminoacids.rtp  ffnonbonded.itp
>> aminoacids.hdbatomtypes.atp   forcefield.doc
>> aminoacids.n.tdb  ffbonded.itpforcefield.itp
>>
>>
> For some reason the tarball is missing several files, notably the .r2b
> file that prevents the error you are seeing.  I uploaded a new tarball with
> the full file set.  Please download it and try again.
>
> -Justin
>
>
>  I wonder why I am getting the same error as HISE not found. Also the
>> pdb2gmx reads the input file and stops reading when it encounters the
>> phosphorylated serine's coordinates, notated as SEP. So is it the correct
>> spot to unpack the phosphorylated files?
>> Thanks
>> JJ
>>
>>
>> On Mon, Nov 17, 2014 at 10:29 AM, Justin Lemkul  wrote:
>>
>>
>>>
>>> On 11/16/14 8:26 PM, Jayant James wrote:
>>>
>>>  Hi !
 I downloaded the ffG43a1p.tar.gz
  for
 simulations of phosphorylated serines (downloaded from
 http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
 running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
 error (below). Well there is no "HISE" in the input pdb file. There is a
 SEP. So I thought I'd better get help from the GMX community. I also
 found
 that if I were to execute a pdb file without any phosphorylated serine
 the
 pdb2gmx runs all the way to the end and the gives the error message
 similar
 to one below.


  You downloaded the wrong files.  Note there is a specific version for
>>> 4.5
>>> and onward:
>>>
>>> http://www.gromacs.org/@api/deki/files/132/=gromos43a1p-4.5.1.tgz
>>>
>>> -Justin
>>>
>>> --
>>> ==
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==
>>> --
>>> 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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>>> 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.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Balt

Re: [gmx-users] Updated CHARMM36 force field files available

2014-11-17 Thread Justin Lemkul




On 11/17/14 4:22 PM, Guillaume Chevrot wrote:


Le 17/11/2014 18:32, Justin Lemkul a écrit :



On 11/17/14 6:04 AM, Guillaume Chevrot wrote:

Dear Justin,

thanks for the new version of the charmm36 force field.

I have a question concerning the file merged.hdb.
I noticed that ADP has disappeared from this file. As consequence, pdb2gmx now
(it was not the case with previous release charmm36-mar2014) complains:
WARNING: atom H4' is missing in residue ADP 

Is there a good reason to have made this modification?



It wasn't removed; our released force fields have never had ADP in the .hdb
file.  The .hdb is written manually, so it doesn't cover everything in the
.rtp file.


OK. So maybe it could also be added in the next release by default? If I can
help ...



The .hdb for ADP would be the same as ADE, unless you're doing something 
non-physiological with the phosphate protonation states.  Then it's simply 
hydroxyl syntax.


I can certainly add it, but we're still not covering about 90% of the chemical 
space that the .rtp does.  At best, we provide building blocks for the most 
common biopolymers, otherwise it's a never-ending battle for .hdb writing which, 
as I said, manual.  Unless we figure out some very clever way to construct .hdb 
from .rtp, then I can never hope to deliver everything in both files.  Of 
course, if anyone has any brilliant insights on converting CHARMM .rtf to 
GROMACS .hdb using Python (which is what our converter is written in right now), 
I'm all ears...


-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Updated CHARMM36 force field files available

2014-11-17 Thread Guillaume Chevrot



Le 17/11/2014 18:32, Justin Lemkul a écrit :



On 11/17/14 6:04 AM, Guillaume Chevrot wrote:

Dear Justin,

thanks for the new version of the charmm36 force field.

I have a question concerning the file merged.hdb.
I noticed that ADP has disappeared from this file. As consequence, 
pdb2gmx now

(it was not the case with previous release charmm36-mar2014) complains:
WARNING: atom H4' is missing in residue ADP 

Is there a good reason to have made this modification?



It wasn't removed; our released force fields have never had ADP in the 
.hdb file.  The .hdb is written manually, so it doesn't cover 
everything in the .rtp file.


OK. So maybe it could also be added in the next release by default? If I 
can help ...





I also noticed that there is no entry in merged.hdb for TP2 (the 
dianionic

phosphotyrosine).



I will add these for the next release.  For the dianionic species, the 
.hdb will be the same as the unphosphorylated residue, minus the 
hydroxyl H.  The monoanionic are the same, with hydroxyl syntax for 
the HPO4 atom the same as any other hydroxyl.  Let me know if you need 
help adding these.


Thanks, I had already added the entry I needed. I was just a bit 
surprised it was not already there.



Guillaume


-Justin



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Re: [gmx-users] problem with phosphorylated serine

2014-11-17 Thread Justin Lemkul




On 11/17/14 1:25 PM, Jayant James wrote:

Hi!
I had actually downloaded the *gromos43a1p-4.5.1.tgz (47 KB) file, *it
was not the ffG43a1p.tar.gz as said earlier. Sorry about the
miscommunication.
So *gromos43a1p-4.5.1.tgz *file was unpacked and placed in

/share/apps/gromacs/4.5.4/single/share/gromacs/top/ and it creates the
gromos43a1p.ff directory. Under the directory are the files

aminoacids.c.tdb  aminoacids.rtp  ffnonbonded.itp
aminoacids.hdbatomtypes.atp   forcefield.doc
aminoacids.n.tdb  ffbonded.itpforcefield.itp



For some reason the tarball is missing several files, notably the .r2b file that 
prevents the error you are seeing.  I uploaded a new tarball with the full file 
set.  Please download it and try again.


-Justin


I wonder why I am getting the same error as HISE not found. Also the
pdb2gmx reads the input file and stops reading when it encounters the
phosphorylated serine's coordinates, notated as SEP. So is it the correct
spot to unpack the phosphorylated files?
Thanks
JJ


On Mon, Nov 17, 2014 at 10:29 AM, Justin Lemkul  wrote:




On 11/16/14 8:26 PM, Jayant James wrote:


Hi !
I downloaded the ffG43a1p.tar.gz
 for
simulations of phosphorylated serines (downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
error (below). Well there is no "HISE" in the input pdb file. There is a
SEP. So I thought I'd better get help from the GMX community. I also found
that if I were to execute a pdb file without any phosphorylated serine the
pdb2gmx runs all the way to the end and the gives the error message
similar
to one below.



You downloaded the wrong files.  Note there is a specific version for 4.5
and onward:

http://www.gromacs.org/@api/deki/files/132/=gromos43a1p-4.5.1.tgz

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] problem with phosphorylated serine

2014-11-17 Thread Jayant James

Hi!
I had actually downloaded the *gromos43a1p-4.5.1.tgz (47 KB) file, *it
was not the ffG43a1p.tar.gz as said earlier. Sorry about the
miscommunication.
So *gromos43a1p-4.5.1.tgz *file was unpacked and placed in

/share/apps/gromacs/4.5.4/single/share/gromacs/top/ and it creates the
gromos43a1p.ff directory. Under the directory are the files

aminoacids.c.tdb  aminoacids.rtp  ffnonbonded.itp
aminoacids.hdbatomtypes.atp   forcefield.doc
aminoacids.n.tdb  ffbonded.itpforcefield.itp

I wonder why I am getting the same error as HISE not found. Also the
pdb2gmx reads the input file and stops reading when it encounters the
phosphorylated serine's coordinates, notated as SEP. So is it the correct
spot to unpack the phosphorylated files?
Thanks
JJ

On Mon, Nov 17, 2014 at 10:29 AM, Justin Lemkul  wrote:

>
>
> On 11/16/14 8:26 PM, Jayant James wrote:
>
>> Hi !
>> I downloaded the ffG43a1p.tar.gz
>>  for
>> simulations of phosphorylated serines (downloaded from
>> http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
>> running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
>> error (below). Well there is no "HISE" in the input pdb file. There is a
>> SEP. So I thought I'd better get help from the GMX community. I also found
>> that if I were to execute a pdb file without any phosphorylated serine the
>> pdb2gmx runs all the way to the end and the gives the error message
>> similar
>> to one below.
>>
>>
> You downloaded the wrong files.  Note there is a specific version for 4.5
> and onward:
>
> http://www.gromacs.org/@api/deki/files/132/=gromos43a1p-4.5.1.tgz
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
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>
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>

-- 
Jayasundar Jayant James

http://www.chick.com/reading/tracts/0076/0076_01.asp
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Re: [gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

2014-11-17 Thread Bruce D. Ray

On Mon, 17 Nov 2014, at 18:54:00 +0330, leila karami  
wrote:
>Dear gromacs users
>
>I installed topolbuild version 1.3. I used following command line:
>
>./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas
>
>I encountered with following error:
>
>Fatal error.
>Source code file: readmol2.c, line: 162
>Atomic symbol O2 in atom type not found.
>
>How to resolve this problem?
>
>Any help will highly appreciated.

I have pasted youyr mol2 file from your second message below.

On Mon, 17 Nov 2014, at 18:56:00 +0330, leila karami  
wrote:
>my mol2file is as follows:
>
>  @MOLECULE
>C:\Users\scc\Desktop\22.pdb
> 30 31 0 0 0
>SMALL
>GASTEIGER
>
>@ATOM
>  1  O2 0.99910.0511   -0.0859 O2  1  C1 -0.2444
>  2  C2 2.22660.0511   -0.0859 Car 1  C1  0.3522
>  3  N3 2.87602.9655   -4.9849 Nar 1  C1 -0.1783
>  4  C4 2.22662.3904   -4.0182 Car 1  C1  0.1230
>  5  N4 0.83012.3904   -4.0182 Npl 1  C1 -0.3430
>  6  C5 2.89811.7958   -3.0187 Car 1  C1 -0.0056
>  7  C6 2.22661.2012   -2.0192 Car 1  C1  0.0152
>  8  N1 2.87600.6262   -1.0526 Nar 1  C1 -0.2700
>  9  C1*4.31050.6262   -1.0526 C3  1  C1  0.1680
> 10  H1*4.66721.1419   -1.9196 H   1  C1  0.0867
> 11  O4*6.2372   -0.7744   -3.5532 O3  1  C1 -0.3456
> 12  C4*4.8172   -0.7744   -3.5532 C3  1  C1  0.1126
> 13  H4*4.4605   -1.2673   -4.4334 H   1  C1  0.0647
> 14  C3*4.3105   -1.5070   -2.3216 C3  1  C1  0.1135
> 15  H3*3.2405   -1.5070   -2.3216 H   1  C1  0.0647
> 16  O3*4.7839   -2.8457   -2.3391 O3  1  C1 -0.3864
> 17  C2*4.8172   -0.8068   -1.0713 C3  1  C1  0.1286
> 18  H2*5.8872   -0.8068   -1.0713 H   1  C1  0.0665
> 19  O2*4.3439   -1.49130.0793 O3  1  C1 -0.3847
> 20  C5*4.31050.6586   -3.5345 C3  1  C1  0.0730
> 21  O5*2.89050.6586   -3.5345 O3  1  C1 -0.3924
> 22  H410.33011.9477   -3.2739 H   1  C1  0.1437
> 23  H420.33012.8332   -4.7625 H   1  C1  0.1437
> 24  H5 3.93011.7958   -3.0187 H   1  C1  0.0666
> 25  H6 1.19461.2012   -2.0192 H   1  C1  0.0812
> 26  H3*5.7839   -2.8457   -2.3391 HO  1  C1  0.2100
> 27  H2*4.6772   -2.43400.0670 HO  1  C1  0.2101
> 28 H5*14.66721.1515   -2.6543 H   1  C1  0.0584
> 29 H5*24.66721.1743   -4.4015 H   1  C1  0.0584
> 30  H5*2.55720.1979   -4.3571 HO  1  C1  0.2095
>@BOND
> 1 1 22
> 2 2 3   ar
> 3 2 8   ar
> 4 3 4   ar
> 5 4 51
> 6 4 6   ar
> 7 5221
> 8 5231
> 9 6 7   ar
>10 6241
>11 7 8   ar
>12 7251
>13 8 91
>14 9111
>15 9171
>16 9101
>1711121
>1812131
>1912141
>2012201
>2114171
>2214161
>2314151
>2416261
>2517181
>2617191
>2719271
>2820211
>2920281
>3020291
>3121301

The first thing I notice about this mol2 file is that none of the atom types 
given in
the sixth column are valid Tripos Sybyl atom types.  For example, for the first 
four
atoms, the valid Tripos Sybyl atom types would be O.2, C.ar, N.ar, C.ar, and 
N.pl
Notice the "." character that separates the element from the type modifier.  
The program
searches for that character to determine what the element is, what bonding to 
expect,
and how to convert this information to the correct atom type for the topology.

The second thing I notice is that the mol2 file is not properly terminated.  
After the
last bond record is given, you need a line that reads @   In a complete
mol2 file, this is typically @SUBSTRUCTURE  The program only looks for 
the
@ portion to be sure that everything needed is read.

Third, it appears that this file was created on a Windows machine.  You might 
need to
run dos2unix on it to get the correct line terminatiions.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202-3273
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Re: [gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

2014-11-17 Thread Justin Lemkul




On 11/17/14 10:24 AM, leila karami wrote:

Dear gromacs users

I installed topolbuild version 1.3. I used following command line:

./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas

I encountered with following error:

Fatal error.
Source code file: readmol2.c, line: 162
Atomic symbol O2 in atom type not found.

How to resolve this problem?



O2 is not a valid atom type, but O.2 is.

http://www.tripos.com/mol2/atom_types.html

-Justin

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Re: [gmx-users] (no subject)

2014-11-17 Thread Justin Lemkul




On 11/17/14 9:15 AM, behnaz abdolmaleki wrote:

Dear all

I want to calculate free energy by g_lie, but I do not know how to select
the length of  box for free ligand simulation.should I select the dimension
of box for ligand simulation (in free situation ) as same as the dimension
of box in complex simulation (receptor-ligand)? or I can do whit another
lenght ?



The box just needs to be large enough to avoid minimum image violations, like 
any other simulation; the goal there is to obtain nonbonded interaction energies 
between the ligand and solvent, so it's not particularly special in its setup.


-Justin

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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
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Re: [gmx-users] Protein comparison

2014-11-17 Thread Justin Lemkul




On 11/17/14 8:09 AM, Onur Tuna wrote:

Dear md,

I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change?

You can perform binding energy calculation, of course. You have a docked
structure. First make sure your docking simulation is reliable. It is
important which software you have used and what kind of protein and ligand
you have. After making sure your docking result is reliable you have to carry
out MD simulation for testing whether your complex structure is stable. From
MD simulations you are able to carry out analysis: what kind of interactions
you have? Charged groups, Hydrogen bonding etc. After making sure your
structure is stable during MD simulation (you can check RMSD values for this)
you are able to calculate Potential of Mean Force using Umbrella Sampling or
you can perform Free Energy Perturbation calculations.



In addition, one must take great care to properly parametrize the ligand for MD 
simulation if the results are to be of any use.


-Justin


Please explore your structure and make sure your docking result is proper
firstly.

Best, Onur


On 17 Nov 2014, at 13:42, rama david  wrote:

Dear MD,


You are asking this question again. but let to tell you, the energy
comparison are made by docking software. Please see the manual of software
and mentioned the name of software you are using.

By gromacs you can do the MD simulation and do analysis of other
interaction pattern.

You cant compare just docking result  in gromacs.




On Mon, Nov 17, 2014 at 9:37 AM, md kashif mailto:kashifzamir180...@gmail.com>> wrote:


Dear all I have protein pdb file and protein+ligand pdb file generated
after docking. How can I compare them by using gromacs? With the word
"compare " I mean that what kind of analysis I can perform? Should I
perform binding energy calculation or rmsd calculation for protein
stability change? Kindly suggest any tutorial for help.

Thanks


On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:


Dear all I have protein pdb file and protein+ligand pdb file generated
after docking. How can I compare them by using gromacs?

Thanks


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==

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Re: [gmx-users] adding ions in Gromacs 4.6.5

2014-11-17 Thread Justin Lemkul




On 11/17/14 6:42 AM, soumadwip ghosh wrote:

Dear all,
   I am currently working on  double stranded DNA aggregation
and I require to add tetramethyl ammonium ions in my system. I know there
are certain files to be modified in the force field directory for this
purpose but I dont know which files. I am using Gromacs 4.6.5 and Charmm 27
forcefield. I created the following pdb file using Gauss view 5.0.8. I will
be highly obliged if someone tells me how and which files are to be
modified to run the simulations in presence of this ion,



You don't need to modify force field files to simulate this species, you just 
need to generate a topology (.itp) for it.  You only need to modify the force 
field if you're adding a new building block for pdb2gmx or if you need to add 
new atom types (which for tetramethylammonium in CHARMM you should not have to).


-Justin




TITLE   Required
REMARK   1 File created by GaussView 5.0.8
HETATM1  N   0   3.666  -1.350  -1.577
   N
HETATM2  C   0   4.157  -0.657  -2.777
   C
HETATM3  H   0   5.227  -0.657  -2.777
   H
HETATM4  H   0   3.800  -1.161  -3.651
   H
HETATM5  H   0   3.800   0.352  -2.777
   H
HETATM6  C   0   4.156  -0.657  -0.377
   C
HETATM7  H   0   3.800   0.352  -0.377
   H
HETATM8  H   0   3.800  -1.161   0.497
   H
HETATM9  H   0   5.226  -0.657  -0.377
   H
HETATM   10  C   0   4.156  -2.736  -1.577
   C
HETATM   11  H   0   3.800  -3.240  -2.451
   H
HETATM   12  H   0   5.226  -2.736  -1.577
   H
HETATM   13  H   0   3.799  -3.240  -0.703
   H
HETATM   14  C   0   2.196  -1.350  -1.577
   C
HETATM   15  H   0   1.840  -0.341  -1.577
   H
HETATM   16  H   0   1.840  -1.854  -2.451
   H
HETATM   17  H   0   1.840  -1.854  -0.703
   H
END
CONECT126   10   14
CONECT21345
CONECT32
CONECT42
CONECT52
CONECT61789
CONECT76
CONECT86
CONECT96
CONECT   101   11   12   13
CONECT   11   10
CONECT   12   10
CONECT   13   10
CONECT   141   15   16   17
CONECT   15   14
CONECT   16   14
CONECT   17   14

Thanks in advance
Soumadwip Ghosh
Senior research fellow,
Indian institute Of Technology, Bombay,
India



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==

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Re: [gmx-users] Updated CHARMM36 force field files available

2014-11-17 Thread Justin Lemkul




On 11/17/14 6:04 AM, Guillaume Chevrot wrote:

Dear Justin,

thanks for the new version of the charmm36 force field.

I have a question concerning the file merged.hdb.
I noticed that ADP has disappeared from this file. As consequence, pdb2gmx now
(it was not the case with previous release charmm36-mar2014) complains:
WARNING: atom H4' is missing in residue ADP 

Is there a good reason to have made this modification?



It wasn't removed; our released force fields have never had ADP in the .hdb 
file.  The .hdb is written manually, so it doesn't cover everything in the .rtp 
file.




I also noticed that there is no entry in merged.hdb for TP2 (the dianionic
phosphotyrosine).



I will add these for the next release.  For the dianionic species, the .hdb will 
be the same as the unphosphorylated residue, minus the hydroxyl H.  The 
monoanionic are the same, with hydroxyl syntax for the HPO4 atom the same as any 
other hydroxyl.  Let me know if you need help adding these.


-Justin

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Re: [gmx-users] problem with phosphorylated serine

2014-11-17 Thread Justin Lemkul




On 11/16/14 8:26 PM, Jayant James wrote:

Hi !
I downloaded the ffG43a1p.tar.gz
 for
simulations of phosphorylated serines (downloaded from
http://www.gromacs.org/Downloads/User_contributions/Force_fields). Upon
running the pdb2gmx command in gromacs version VERSION 4.5.4. I get this
error (below). Well there is no "HISE" in the input pdb file. There is a
SEP. So I thought I'd better get help from the GMX community. I also found
that if I were to execute a pdb file without any phosphorylated serine the
pdb2gmx runs all the way to the end and the gives the error message similar
to one below.



You downloaded the wrong files.  Note there is a specific version for 4.5 and 
onward:


http://www.gromacs.org/@api/deki/files/132/=gromos43a1p-4.5.1.tgz

-Justin

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Re: [gmx-users] Umbrella Sampling and flat-bottom position restraints

2014-11-17 Thread Justin Lemkul




On 11/16/14 5:44 PM, Oliver Stueker wrote:

Hi Justin,

Thanks for the feedback.

On Sun, Nov 16, 2014 at 2:51 PM, Justin Lemkul  wrote:




On 11/16/14 1:04 PM, Oliver Stueker wrote:


Dear fellow Gromacs Users,

I'm trying to calculate the binding free energy between a protein and a
small molecule using Umbrella Sampling.

I made my first attempt last year using Gromacs 4.5 and ran into the same
convergence problems that have been pointed out on the mailing list
several
times.
To overcome these problems I now want to give it another try utilizing the
flat-bottomed position restraints that have been introduced in Gromacs
5.0.

My plan is to perform the Umbrella sampling along the Z-axis and to
restrict the protein as well as the ligand with flat-bottomed position
restraints along X and Y into a cylindrical space (as suggested e.g. by
Chris Neale in [1]).

But I'm not quite sure what radius the cylinder should have ( or how wide
the flat bottom should be).
The protein is roughly spherical with a diameter of ~4nm. I was initially
thinking to use an r_{fb} of 2nm for the protein and  for the ligand 1/2
of
it's longest dimension to allow both of them to re-orient freely. But the
more I think about, I'm afraid that it's too large.



Why is it necessary to pull only along the z-axis?  For simple ligand
binding to a globular protein, you can define the pull vector in any or all
of the three spatial dimensions.  Is there some reason you presuppose
binding only along z?



Hmm, indeed it's probably not necessary to pull only along Z. However the
box would need to be much larger if I can't control the direction.
In my first attempt I had already aligned the vector between the COMs of
Protein and ligand with the Z-axis so that I can pull along that direction.
That time I've used a box of 10 x 10 x 15 nm.

Last time I've used the following pull settings:
; Pull code
pull= umbrella
pull_geometry   = distance
pull_dim= N N Y
pull_start  = yes
pull_ngroups= 1
pull_group0 = Protein
pull_group1 = LIG
pull_init1  = 0
pull_rate1  = 0.0
pull_k1 = 1000  ; kJ mol^-1 nm^-2
pull_nstxout= 1000  ; every 2 ps
pull_nstfout= 1000  ; every 2 ps

I also had the problem that during the equillibration of the Umbrella
windows the ligand moved a bit away from it's initial position so that the
initial pull distance was a bit off. This time I want to prevent that by
setting pull_init for each window directly and leave pull_start = off.

Say if I use pull_dim = Y Y Y and a cubic box of 15 x 15 x 15 nm. That
would restrict the ligand to the surface of a sphere of radius d (COM
reference distance of the umbrella window) around the protein. Wouldn't
that mean that I would need to sample the ligand conformations on the
complete surface of each sphere to achieve sufficient conformational
overlap between neighbouring windows? Those surfaces would become quite big
once I reach to high COM distances (6 nm).


More judicious choice of reaction coordinate eliminates this problem.  Unless 
the binding site is coincident with the COM of the protein, it is better to 
choice a few binding site residues as the reference, thus more clearly defining 
the reaction coordinate.  At longer range, anyway, the interactions between the 
ligand and any protein residue are negligible, so I would not think you would 
need to sample the entire sphere around the reference group.  Indeed, this would 
likely require microseconds of sampling, which no one does.



Say if in two windows n-1 and n+1 the ligand moves towards +X / +Y and in
window n (in between) the ligand moves to -X / -Y. Then while the
histograms might overlap nicely (according the sampled COM distances) the
sampled conformations might be very different.



True, but the spacing of the windows in this case also depends on the 
flexibility of the ligand.



It seems that simply using pull_dim = Y Y Y would also not really solve
the problem.



I disagree.  I think the choice of z-only pull in the case of a free-floating 
ligand is making a large assumption, and one based solely on convenience.  Note 
that this is a very different case from my tutorial, in which uni-directional, 
linear growth of an aggregate is experimentally proven; so don't lock yourself 
into that thinking too much.






  Has anyone have experience with that? Maybe even a published paper?

So far I've unsuccessfully tried several times to find a published method.


Also to I need to consider the flat-bottomed potential when doing the
g_wham analysis?



It's an additional bias to the Hamiltonian, so it should probably be
accounted for in some way.  As to how, I'm not sure.  But it's an
additional degree of freedom that is being restrained.



Yes, you are probably right.

Would this work:

- generate conformations by pulling along Z and select conformations for
windows
- equillibrate each window
- run umbrella-sampling (to sample conforma

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

2014-11-17 Thread leila karami

my mol2file is as follows:

  @MOLECULE
C:\Users\scc\Desktop\22.pdb
 30 31 0 0 0
SMALL
GASTEIGER

@ATOM
  1  O2 0.99910.0511   -0.0859 O2  1  C1 -0.2444
  2  C2 2.22660.0511   -0.0859 Car 1  C1  0.3522
  3  N3 2.87602.9655   -4.9849 Nar 1  C1 -0.1783
  4  C4 2.22662.3904   -4.0182 Car 1  C1  0.1230
  5  N4 0.83012.3904   -4.0182 Npl 1  C1 -0.3430
  6  C5 2.89811.7958   -3.0187 Car 1  C1 -0.0056
  7  C6 2.22661.2012   -2.0192 Car 1  C1  0.0152
  8  N1 2.87600.6262   -1.0526 Nar 1  C1 -0.2700
  9  C1*4.31050.6262   -1.0526 C3  1  C1  0.1680
 10  H1*4.66721.1419   -1.9196 H   1  C1  0.0867
 11  O4*6.2372   -0.7744   -3.5532 O3  1  C1 -0.3456
 12  C4*4.8172   -0.7744   -3.5532 C3  1  C1  0.1126
 13  H4*4.4605   -1.2673   -4.4334 H   1  C1  0.0647
 14  C3*4.3105   -1.5070   -2.3216 C3  1  C1  0.1135
 15  H3*3.2405   -1.5070   -2.3216 H   1  C1  0.0647
 16  O3*4.7839   -2.8457   -2.3391 O3  1  C1 -0.3864
 17  C2*4.8172   -0.8068   -1.0713 C3  1  C1  0.1286
 18  H2*5.8872   -0.8068   -1.0713 H   1  C1  0.0665
 19  O2*4.3439   -1.49130.0793 O3  1  C1 -0.3847
 20  C5*4.31050.6586   -3.5345 C3  1  C1  0.0730
 21  O5*2.89050.6586   -3.5345 O3  1  C1 -0.3924
 22  H410.33011.9477   -3.2739 H   1  C1  0.1437
 23  H420.33012.8332   -4.7625 H   1  C1  0.1437
 24  H5 3.93011.7958   -3.0187 H   1  C1  0.0666
 25  H6 1.19461.2012   -2.0192 H   1  C1  0.0812
 26  H3*5.7839   -2.8457   -2.3391 HO  1  C1  0.2100
 27  H2*4.6772   -2.43400.0670 HO  1  C1  0.2101
 28 H5*14.66721.1515   -2.6543 H   1  C1  0.0584
 29 H5*24.66721.1743   -4.4015 H   1  C1  0.0584
 30  H5*2.55720.1979   -4.3571 HO  1  C1  0.2095
@BOND
 1 1 22
 2 2 3   ar
 3 2 8   ar
 4 3 4   ar
 5 4 51
 6 4 6   ar
 7 5221
 8 5231
 9 6 7   ar
10 6241
11 7 8   ar
12 7251
13 8 91
14 9111
15 9171
16 9101
1711121
1812131
1912141
2012201
2114171
2214161
2314151
2416261
2517181
2617191
2719271
2820211
2920281
3020291
3121301
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[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

2014-11-17 Thread leila karami

my mol2file is as follows:

  @MOLECULE
C:\Users\scc\Desktop\22.pdb
 30 31 0 0 0
SMALL
GASTEIGER

@ATOM
  1  O2 0.99910.0511   -0.0859 O2  1  C1 -0.2444
  2  C2 2.22660.0511   -0.0859 Car 1  C1  0.3522
  3  N3 2.87602.9655   -4.9849 Nar 1  C1 -0.1783
  4  C4 2.22662.3904   -4.0182 Car 1  C1  0.1230
  5  N4 0.83012.3904   -4.0182 Npl 1  C1 -0.3430
  6  C5 2.89811.7958   -3.0187 Car 1  C1 -0.0056
  7  C6 2.22661.2012   -2.0192 Car 1  C1  0.0152
  8  N1 2.87600.6262   -1.0526 Nar 1  C1 -0.2700
  9  C1*4.31050.6262   -1.0526 C3  1  C1  0.1680
 10  H1*4.66721.1419   -1.9196 H   1  C1  0.0867
 11  O4*6.2372   -0.7744   -3.5532 O3  1  C1 -0.3456
 12  C4*4.8172   -0.7744   -3.5532 C3  1  C1  0.1126
 13  H4*4.4605   -1.2673   -4.4334 H   1  C1  0.0647
 14  C3*4.3105   -1.5070   -2.3216 C3  1  C1  0.1135
 15  H3*3.2405   -1.5070   -2.3216 H   1  C1  0.0647
 16  O3*4.7839   -2.8457   -2.3391 O3  1  C1 -0.3864
 17  C2*4.8172   -0.8068   -1.0713 C3  1  C1  0.1286
 18  H2*5.8872   -0.8068   -1.0713 H   1  C1  0.0665
 19  O2*4.3439   -1.49130.0793 O3  1  C1 -0.3847
 20  C5*4.31050.6586   -3.5345 C3  1  C1  0.0730
 21  O5*2.89050.6586   -3.5345 O3  1  C1 -0.3924
 22  H410.33011.9477   -3.2739 H   1  C1  0.1437
 23  H420.33012.8332   -4.7625 H   1  C1  0.1437
 24  H5 3.93011.7958   -3.0187 H   1  C1  0.0666
 25  H6 1.19461.2012   -2.0192 H   1  C1  0.0812
 26  H3*5.7839   -2.8457   -2.3391 HO  1  C1  0.2100
 27  H2*4.6772   -2.43400.0670 HO  1  C1  0.2101
 28 H5*14.66721.1515   -2.6543 H   1  C1  0.0584
 29 H5*24.66721.1743   -4.4015 H   1  C1  0.0584
 30  H5*2.55720.1979   -4.3571 HO  1  C1  0.2095
@BOND
 1 1 22
 2 2 3   ar
 3 2 8   ar
 4 3 4   ar
 5 4 51
 6 4 6   ar
 7 5221
 8 5231
 9 6 7   ar
10 6241
11 7 8   ar
12 7251
13 8 91
14 9111
15 9171
16 9101
1711121
1812131
1912141
2012201
2114171
2214161
2314151
2416261
2517181
2617191
2719271
2820211
2920281
3020291
3121301 
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[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

2014-11-17 Thread leila karami

Dear gromacs users

I installed topolbuild version 1.3. I used following command line:

./topolbuild -n khob -dir ../dat/gromacs/ -ff gmx53a6.dat -meas

I encountered with following error:

Fatal error.
Source code file: readmol2.c, line: 162
Atomic symbol O2 in atom type not found.

How to resolve this problem?

Any help will highly appreciated.
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[gmx-users] (no subject)

2014-11-17 Thread behnaz abdolmaleki

Dear all

I want to calculate free energy by g_lie, but I do not know how to select
the length of  box for free ligand simulation.should I select the dimension
of box for ligand simulation (in free situation ) as same as the dimension
of box in complex simulation (receptor-ligand)? or I can do whit another
lenght ?

any help is appreciated
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Re: [gmx-users] Flat-bottomed position restraint set

2014-11-17 Thread Oliver Stueker

> 
> 
> Dose it means that the position restraints are applied to all the oxyen
> atoms of  the water molecules ?


Yes, that should work.

Have a look at http://manual.gromacs.org/programs/gmx-grompp.html (third
paragraph of the description and the -pp flag) and the chapters 5.7.1 and
5.7.3  in the gromacs manual.

Or simply run a short simulation with a few water molecules and a small
sphere-radius. Then you would have had your answer in ~10 minutes  instead
of waiting 12 hours. ;-)

Best,
Oliver



On Sun, Nov 16, 2014 at 10:21 PM, liuyong_1...@dicp.ac.cn <
liuyong_1...@dicp.ac.cn> wrote:

> Dear Oliver,
>
> From you explaination, I modify the equil.mdp file as
>define = -DPOSRES_WATER
>
> and the topol.top file as :
>
> ; Include forcefield parameters
> #include "amber94.ff/forcefield.itp"
>
> [ moleculetype ]
> ; Namenrexcl
> Ion 3
>
> [ atoms ]
> ;   nr   type  resnr residue  atom   cgnr charge   mass
> typeBchargeB  massB
> ; residue   1 NA  rtp NA   q +1.0
>  1 Na  1 NA NA  1  1  22.99   ;
> qtot 1
>
> ; Include topology for ions
> #include "amber94.ff/ions.itp"
>
> #ifdef POSRES_ion
> [ position_restraints ]
> ;  i funct   g r(nm)   k
> ;   121  3.0   30.0
> #endif
>
>
> ; Include water topology
> #include "amber94.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct   g r(nm)   k
>121  3.0   30.0
> ;   221  3.0   30.0
> ;   321  3.0   30.0
> #endif
>
> 
> Dose it means that the position restraints are applied to all the oxyen
> atoms of  the water molecules ?
>
> Best regards,
> Yong Liu
>
>
>
> liuyong_1...@dicp.ac.cn
>
> From: Oliver Stueker
> Date: 2014-11-17 00:46
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Flat-bottomed position restraint set
> Dear Liuyoung,
>
>
> in your equil.mdp
>  you have 
> :
>
> > define  = -D
> > 
> > *POSRES*
>
> 
>
> and in your topol.top:
> 
>
>
> > #ifdef
> > *POSRES_WATER*
> > ; Position restraint for each water oxygen
> > ;[ position_restraints ]
> > ;  i funct   fcxfcyfcz
> > ;  11   1000   1000   1000
> > [ position_restraints ]
> > ;  i funct   g r(nm)   k
> >121  3.0   30.0
> > ;   221  3.0   30.0
> > ;   321  3.0   30.0
> > #endif
>
>
> That means your position_restraints directive will not be included.
>
> Use whatever word you like for both the define and ifdef line, as long as
> it's the same.
> e.g. define -DPOSRES  and  #ifdef POSRES
> or define -DPOSRES_FLATBOTTOM and #ifdef POSRES_FLATBOTTOM
>
>
> Best,
> Oliver
>
>
>
> On Sat, Nov 15, 2014 at 11:11 PM, liuyong_1...@dicp.ac.cn <
> liuyong_1...@dicp.ac.cn> wrote:
>
> > The content of the equil.mdp and topol.top files is shown as follow.
> >
> > 
> > equil.mdp:
> >
> > title   = NVT Equilibration for Na in 56 water
> > ; Run parameters
> > integrator  = md; leap-frog integrator
> > nsteps  = 25000 ; 2 * 50,000 = 100 ps ;(100 ns)
> > dt  = 0.002 ; 2 fs
> > 
> > define  = -DPOSRES
> > ; Output control
> > nstxout = 500   ; save coordinates every 0.1 ps
> > nstvout = 500   ; save velocities every 1 ps
> > nstenergy   = 500   ; save energies every 1 ps
> > nstlog  = 500   ; update log file every 1 ps
> > nstxtcout= 500
> > xtc-precision= 1000
> > ; Bond parameters
> > continuation= yes   ; Restarting after NVT
> > constraint_algorithm = ; holonomic constraints
> > constraints =h-angles   ;water both bond and angle constrained
> > ;constraints= hbonds; all bonds (even heavy atom-H bonds)
> > constrained
> > lincs_iter  = 1 ; accuracy of LINCS
> > lincs_order = 4 ; also related to accuracy
> > ; Neighborsearching
> > ns_type = grid  ; search neighboring grid cels
> > nstlist = 1 ; 10 fs
> > rlist   = 1.0   ; short-range neighborlist cutoff (in nm)
> > ; vdw
> > vdw-type = Cut-off
> > rvdw= 3.0   ; short-range van der Waals cutoff (in nm)
> > ; Electrostatics
> > coulombtype = cut-off ;Reaction-Field ;Generalized-Reaction-Field
> ;cut-off
> > rcoulomb= 3.0   ; short-range electrostatic cutoff (in nm)
> > epsilon_rf  = 2.0
> > epsilon_r   = 0.5
> > cutoff-scheme   = group
> > ;pme_order  = 4 ; cubic interpolation
> > ;fourierspacing = 0.16  ; grid spacing for FFT
> > ; Temperature coupling is on
> > ; annealing = single
> > ; annealing_time = 0 40016002400  4000  5600   7200  10400
> > 13600  16800 ; 230  260  270  300  330   360
> > ; annealing_temp  =0 20  40 6

Re: [gmx-users] Protein comparison

2014-11-17 Thread Onur Tuna

Dear md,

I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change?

You can perform binding energy calculation, of course. You have a docked 
structure. First make sure your docking simulation is reliable. It is important 
which software you have used and what kind of protein and ligand you have. 
After making sure your docking result is reliable you have to carry out MD 
simulation for testing whether your complex structure is stable. From MD 
simulations you are able to carry out analysis: what kind of interactions you 
have? Charged groups, Hydrogen bonding etc. After making sure your structure is 
stable during MD simulation (you can check RMSD values for this) you are able 
to calculate Potential of Mean Force using Umbrella Sampling or you can perform 
Free Energy Perturbation calculations.

Please explore your structure and make sure your docking result is proper 
firstly.

Best,
Onur

> On 17 Nov 2014, at 13:42, rama david  wrote:
> 
> Dear MD,
> 
> 
> You are asking this question again. but let to tell you,
> the energy comparison are made by docking software. Please
> see the manual of software and mentioned the name of software you are using.
> 
> By gromacs you can do the MD simulation and do analysis of other
> interaction pattern.
> 
> You cant compare just docking result  in gromacs.
> 
> 
> 
> 
> On Mon, Nov 17, 2014 at 9:37 AM, md kashif  >
> wrote:
> 
>> Dear all
>> I have protein pdb file and protein+ligand pdb file generated after
>> docking. How can I compare them by using gromacs? With the word "compare "
>> I mean that what kind of analysis I can perform? Should I perform binding
>> energy calculation or rmsd calculation for protein stability change? Kindly
>> suggest any tutorial for help.
>> 
>> Thanks
>> 
>> 
>> On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
>> wrote:
>> 
>>> Dear all
>>> I have protein pdb file and protein+ligand pdb file generated after
>>> docking. How can I compare them by using gromacs?
>>> 
>>> Thanks
>>> 
>> --
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> 
> 
> 
> 
> Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu 
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Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu 
e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde 
kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin 
icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez.

The information contained in this communication may contain confidential or 
legally privileged information. Hacettepe University doesn't accept any legal 
responsibility for the contents and attachments of this message. The sender 
does not accept any liability for any errors or omissions or any viruses in the 
context of this message which arise as a result of internet transmission.
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Re: [gmx-users] ramachandran plot

2014-11-17 Thread Tsjerk Wassenaar

Hi Urszula,

Save the following as kde2d.r and make it executable. Then you can run

./kde2d.r rama.dat rama.png

Cheers,

Tsjerk

kde2d.r

#!/usr/bin/env Rscript

# Script for drawing 2D combined linear/circular KDE plots.
#
# (c)2014 Tsjerk A. Wassenaar
# Friedrich-Alexander University of Erlangen-Nuremberg

args <- commandArgs()
args <- args[-(1:match("--args", args))]

# MASS library is needed for bandwidths
require(MASS)

# This 2D circular KDE function was developed for correct handling
# of bivariate angular data as part of the orientational analysis
# used with DAFT (Manuscript submitted).
kde2d <- function (x, y, h, n = 25, xlim, ylim, circular=TRUE, phase=0)
{
if (length(y) != length(x))
stop("data vectors must be the same length")

n<- rep(n, length.out = 2L)
phase<- rep(phase, length.out = 2L)
circular <- rep(circular, length.out = 2L)

s <- which(!is.na(x) | !is.na(y))
x <- x[s]
y <- y[s]

nx <- length(x)

if (any(!is.finite(x)) || any(!is.finite(y)))
stop("missing or infinite values in the data are not allowed")

if (circular[1])
x <- (x+180)%%360-180

if (circular[2])
y <- (y+180)%%360-180

if (missing(xlim))
xlim <- if (circular[1]) c(-180,180) else range(x)

if (missing(ylim))
ylim <- if (circular[2]) c(-180,180) else range(y)

if (any(!is.finite(c(xlim,ylim
stop("only finite values are allowed in 'xlim' and 'ylim'")

h <- if (missing(h))
c(bandwidth.nrd(x), bandwidth.nrd(y))
else rep(h, length.out = 2L)
if (any(h <= 0))
stop("bandwidths must be strictly positive")
h <- h/4

if (circular[1])
{
gx <- seq.int(-180, 180, length.out = n[1L])
ax <- ((outer(gx, x-phase[1], "-")+180)%%360-180)/h[1L]
gx <- gx + phase[1]
}
else
{
gx <- seq.int(xlim[1], xlim[2], length.out = n[1L])
ax <- outer(gx, x, "-")/h[1L]
}

if (circular[2])
{
gy <- seq.int(-180, 180, length.out = n[2L])
ay <- ((outer(gy, y-phase[2], "-")+180)%%360-180)/h[2L]
gy <- gy + phase[2]
}
else
{
gy <- seq.int(ylim[1], ylim[2], length.out = n[2L])
ay <- outer(gy, y, "-")/h[2L]
}

z <- tcrossprod(matrix(dnorm(ax), , nx), matrix(dnorm(ay), , nx))/(nx *
h[1L] * h[2L])

list(x = gx, y = gy, z = z)
}

# Color gradients for coloring density plots

rng   <- seq(0,1,length.out=100)

white2red <- rgb(1,rev(rng),rev(rng))
blue2white<- rgb(rng,rng,1)

# Rainbow
magenta2red   <- rgb(1,0,rev(rng))
red2yellow<- rgb(1,rng,0)
yellow2green  <- rgb(rev(rng),1,0)
green2cyan<- rgb(0,1,rng)
cyan2blue <- rgb(0,rev(rng),1)

red2orange<- rgb(1,0.5*rng,0)
orange2yellow <- rgb(1,0.5+0.5*rng,0)

data <- read.table(args[1])
d<- kde2d(data[,1],data[,2])

## Plotting density images

# Here the density images are prepared and written to file. The first one
(WT) is explained in detail:

#---Start of image---

# Wildtype

# Start a 1200x1200 png file, with a font size (for labels) of 40 points
# Changing the resolution requires changing the font size to keep the
relative size.
png(
args[2],
width=1200,
height=1200,
pointsize=40
)

# Write an image of the density for WT
image(
d$x, d$y, d$z, # Image data X/Y and intensity (Z)
zlim=c(0,max(d$z)),# Limits for coloring
xlab=expression(phi),  # X-label text. expression(beta) gives the greek
character
ylab=expression(psi),  # Y-label text.
main="",   # Main title. Can be set to "" to suppress title.
bty="n",   # Surrounding box type. To draw a thicker box,
the box is here suppressed, using "n" for None.
col=c(white2red,red2orange,orange2yellow)
)

box(lwd=3) # Add a box with a thicker line. Change this to
match the resolution of the imge.
# Add points
points(data[,1], data[,2], pch=".", cex=1)

# Add contour lines
contour(
d$x, d$y, d$z,
zlim=c(0,max(d$z)),
add=TRUE,  # If add=FALSE (default), then 'contour' starts
a new plot.
labels="", # Suppress labels on contour lines
labcex=0.001,  # To avoid gaps in the controu lines (because of
the empty label), set the label size very small
nlevels=20,# Number of lines to draw, between range of
'zlim'
lwd=3  # Width of contour lines. Set to 3 to match png
resolution. Change when changing the resolution.
)

# Close the image file, saving it.
dev.off()

#---End of image---

On Mon, Nov 17, 2014 at 1:44 PM, Urszula Uciechowska <
urszula.uciechow...@biotech.ug.edu.pl> wrote:

> Dear Tsjerk,
>
> Could you send me the script again? as I did not find the attachment in
> your previous email.
>
> best regards
> Urszula
>
>
> > Hi Urszula,
> >
> > Attached is an R script for drawing 2D circular or combined
> > circular/linear
> > KDEs. It works as a comm

Re: [gmx-users] ramachandran plot

2014-11-17 Thread Urszula Uciechowska

Dear Tsjerk,

Could you send me the script again? as I did not find the attachment in
your previous email.

best regards
Urszula


> Hi Urszula,
>
> Attached is an R script for drawing 2D circular or combined
> circular/linear
> KDEs. It works as a command line script, taking as arguments a file with
> 2-column data, and an output image file name (./kde2d.r input.dat
> output.png). It's pretty easy to adapt to suit your needs, even if you
> don't know R specifically. I wrote the routine for a manuscript we just
> submitted, where the method is explained in some detail, and if you like
> the images and care to use it for publications, I would be obliged if you
> could reference that paper ("High-Throughput Simulations of Dimer and
> Trimer Assembly of Membrane Proteins. The DAFT approach."). If you run
> into
> problems or have further questions, please let me know.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Nov 14, 2014 at 4:31 PM, Urszula Uciechowska <
> urszula.uciechow...@biotech.ug.edu.pl> wrote:
>
>> Could you please send me the code? It can be on my private email.
>>
>> Thanks a lot
>>
>> Ursuzla
>>
>> > Hi Urszula,
>> >
>> > It's a while ago that I made that one, and I don't have the code at
>> hand.
>> > But it's a combination of a density plot (kde2d) with the points laid
>> > over,
>> > and a polygon to highlight the forbidden region. These days I'm doing
>> > circular 2D KDEs, whic is more correct. I can send the R code for thay
>> if
>> > you want.
>> >
>> > Best,
>> >
>> > Tsjerk
>> > On Nov 14, 2014 12:34 PM, "Urszula Uciechowska" <
>> > urszula.uciechow...@biotech.ug.edu.pl> wrote:
>> >
>> >> Dear Gromacs users,
>> >>
>> >> I generated the ramachandran plot and would like to colour it in
>> xmgrace
>> >> as it was shown in tutorial:
>> >>  http://nmr.chem.uu.nl/~adrien/course/molmod/analysis2.html
>> >>
>> >> Does anyone know how to do it?
>> >>
>> >> Best regards
>> >> Urszula Uciechowska
>> >>
>> >>
>> >>
>> >>
>> >> -
>> >> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> >> http://www.ug.edu.pl/
>> >>
>> >> --
>> >> 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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>> >>
>> >> * 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!
>> >
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>> send
>> > a mail to gmx-users-requ...@gromacs.org.
>> >
>>
>>
>> University of Gdansk and Medical Univesity of Gdansk
>> Department of Molecular and Cellular Biology
>> ul. Kladki 24
>> 80-822 Gdansk
>> Poland
>>
>>
>> -
>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>> http://www.ug.edu.pl/
>>
>> --
>> 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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>>
>> * 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.
>>
>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
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>


University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland


-
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/

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Re: [gmx-users] getting illegal instruction error in gromacs 4.6.4 execution

2014-11-17 Thread Mark Abraham

Hi,

Have you read
http://www.gromacs.org/Documentation/Installation_Instructions_4.6#4.3.1._Portability_aspects
?

Mark

On Mon, Nov 17, 2014 at 12:46 PM, Chaitali Chandratre  wrote:

> Dear Sir,
>
> Gromacs installation is giving illegal instruction error in job run.
>
> I have recompiled it using sse2...earlier it was with avx..and giving error
> on particular nodes..
> but after recompilation also getting same error..
>
> I am compiling with intel compilers.
>
> What steps shall I take further?
>
> Thanks in advance...
>
> --
> With Regards,
>Chaitali
>
> "I know everything happens for a reason...But sometimes I wish I knew what
> the reason was !! "
> --
> Gromacs Users mailing list
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[gmx-users] getting illegal instruction error in gromacs 4.6.4 execution

2014-11-17 Thread Chaitali Chandratre

Dear Sir,

Gromacs installation is giving illegal instruction error in job run.

I have recompiled it using sse2...earlier it was with avx..and giving error
on particular nodes..
but after recompilation also getting same error..

I am compiling with intel compilers.

What steps shall I take further?

Thanks in advance...

-- 
With Regards,
   Chaitali

"I know everything happens for a reason...But sometimes I wish I knew what
the reason was !! "
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Re: [gmx-users] Protein comparison

2014-11-17 Thread rama david

Dear MD,

 You are asking this question again. but let to tell you,
 the energy comparison are made by docking software. Please
see the manual of software and mentioned the name of software you are using.

By gromacs you can do the MD simulation and do analysis of other
interaction pattern.

You cant compare just docking result  in gromacs.

On Mon, Nov 17, 2014 at 9:37 AM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs? With the word "compare "
> I mean that what kind of analysis I can perform? Should I perform binding
> energy calculation or rmsd calculation for protein stability change? Kindly
> suggest any tutorial for help.
>
> Thanks
>
>
> On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
> wrote:
>
> > Dear all
> >  I have protein pdb file and protein+ligand pdb file generated after
> > docking. How can I compare them by using gromacs?
> >
> > Thanks
> >
> --
> Gromacs Users mailing list
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> posting!
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>
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>
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[gmx-users] adding ions in Gromacs 4.6.5

2014-11-17 Thread soumadwip ghosh

Dear all,
  I am currently working on  double stranded DNA aggregation
and I require to add tetramethyl ammonium ions in my system. I know there
are certain files to be modified in the force field directory for this
purpose but I dont know which files. I am using Gromacs 4.6.5 and Charmm 27
forcefield. I created the following pdb file using Gauss view 5.0.8. I will
be highly obliged if someone tells me how and which files are to be
modified to run the simulations in presence of this ion,



TITLE   Required
REMARK   1 File created by GaussView 5.0.8
HETATM1  N   0   3.666  -1.350  -1.577
  N
HETATM2  C   0   4.157  -0.657  -2.777
  C
HETATM3  H   0   5.227  -0.657  -2.777
  H
HETATM4  H   0   3.800  -1.161  -3.651
  H
HETATM5  H   0   3.800   0.352  -2.777
  H
HETATM6  C   0   4.156  -0.657  -0.377
  C
HETATM7  H   0   3.800   0.352  -0.377
  H
HETATM8  H   0   3.800  -1.161   0.497
  H
HETATM9  H   0   5.226  -0.657  -0.377
  H
HETATM   10  C   0   4.156  -2.736  -1.577
  C
HETATM   11  H   0   3.800  -3.240  -2.451
  H
HETATM   12  H   0   5.226  -2.736  -1.577
  H
HETATM   13  H   0   3.799  -3.240  -0.703
  H
HETATM   14  C   0   2.196  -1.350  -1.577
  C
HETATM   15  H   0   1.840  -0.341  -1.577
  H
HETATM   16  H   0   1.840  -1.854  -2.451
  H
HETATM   17  H   0   1.840  -1.854  -0.703
  H
END
CONECT126   10   14
CONECT21345
CONECT32
CONECT42
CONECT52
CONECT61789
CONECT76
CONECT86
CONECT96
CONECT   101   11   12   13
CONECT   11   10
CONECT   12   10
CONECT   13   10
CONECT   141   15   16   17
CONECT   15   14
CONECT   16   14
CONECT   17   14

Thanks in advance
Soumadwip Ghosh
Senior research fellow,
Indian institute Of Technology, Bombay,
India
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Re: [gmx-users] Protein comparison

2014-11-17 Thread Alexander Law

You need to investigate further for your particular system and the questions 
you want answered. Then come back with specific questions and problems. 

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of md kashif 
[kashifzamir180...@gmail.com]
Sent: Monday, November 17, 2014 5:07 PM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Protein comparison

Dear all
 I have protein pdb file and protein+ligand pdb file generated after
docking. How can I compare them by using gromacs? With the word "compare "
I mean that what kind of analysis I can perform? Should I perform binding
energy calculation or rmsd calculation for protein stability change? Kindly
suggest any tutorial for help.

Thanks

On Sun, Nov 16, 2014 at 3:13 PM, md kashif 
wrote:

> Dear all
>  I have protein pdb file and protein+ligand pdb file generated after
> docking. How can I compare them by using gromacs?
>
> Thanks
>
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Re: [gmx-users] Updated CHARMM36 force field files available

2014-11-17 Thread Guillaume Chevrot


Dear Justin,

thanks for the new version of the charmm36 force field.

I have a question concerning the file merged.hdb.
I noticed that ADP has disappeared from this file. As consequence, 
pdb2gmx now (it was not the case with previous release charmm36-mar2014) 
complains:

WARNING: atom H4' is missing in residue ADP 

Is there a good reason to have made this modification?


I also noticed that there is no entry in merged.hdb for TP2 (the 
dianionic phosphotyrosine).



Best,

Guillaume



On 11/06/2014 01:57 AM, Justin Lemkul wrote:


All,

I upload a new version of the GROMACS port for the CHARMM36 force 
field today. You can find the files at:


http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

We have steadily been adding to these files since the last release in 
March. Most fixes are trivial nomenclature adjustments and changes 
related to a few bugs that were propagated in files found in 
charmm27.ff that were subsequently fixed.  All were things that would 
have been obvious because they would have triggered fatal errors when 
running pdb2gmx.


New in this version of the force field are:

1. Changed nucleic acid nomenclature (H5' and H5'') for ease of 
interfacing with CHARMM-GUI
2. New atom type for Mg2+ to use parameters from 
dx.doi.org/10.1021/ct3000734, see MG entry in ions.itp for the 
"define" keyword
3. Addition of phosphorylated amino acids (mono- and dianionic forms 
of Ser, Thr, and Tyr)

4. Addition of bacterial lipids
5. Addition of S-adenosyl methionine

Happy simulating!

-Justin



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Re: [gmx-users] adding ions in Gromacs 4.6.5

[gmx-users] (no subject)

[gmx-users] Umbrella Sampling gromacs 5.0 error

Re: [gmx-users] problem with phosphorylated serine

Re: [gmx-users] problem with phosphorylated serine

Re: [gmx-users] Updated CHARMM36 force field files available

Re: [gmx-users] Updated CHARMM36 force field files available

Re: [gmx-users] problem with phosphorylated serine

Re: [gmx-users] problem with phosphorylated serine

Re: [gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

Re: [gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

Re: [gmx-users] (no subject)

Re: [gmx-users] Protein comparison

Re: [gmx-users] adding ions in Gromacs 4.6.5

Re: [gmx-users] Updated CHARMM36 force field files available

Re: [gmx-users] problem with phosphorylated serine

Re: [gmx-users] Umbrella Sampling and flat-bottom position restraints

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[gmx-users] topolbuild (Fatal error. Source code file: readmol2.c, line: 162)

[gmx-users] (no subject)

Re: [gmx-users] Flat-bottomed position restraint set

Re: [gmx-users] Protein comparison

Re: [gmx-users] ramachandran plot

Re: [gmx-users] ramachandran plot

Re: [gmx-users] getting illegal instruction error in gromacs 4.6.4 execution

[gmx-users] getting illegal instruction error in gromacs 4.6.4 execution

Re: [gmx-users] Protein comparison

[gmx-users] adding ions in Gromacs 4.6.5

Re: [gmx-users] Protein comparison

Re: [gmx-users] Updated CHARMM36 force field files available

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