Re: [gmx-users] dssp doubt

[Emine Deniz Tekin]

Hi Justin,

Thank you for your descriptive reply.

I prepared new index.file which includes mainchain, and when I used the
do_dssp with -n index.ndx, it worked.

But, if I doesn't use the index file, again, the "Protein" is selected by
the system. It is weird..
Best regards,

Deniz
On Thu, Jun 7, 2012 at 5:10 PM, Justin A. Lemkul  wrote:

>
>
> On 6/7/12 10:07 AM, Turgay Cakmak wrote:
>
>> Hi all,
>> I downloaded the original form of DSSP which is recently called
>> DSSPold. Whenever I use the following:
>>
>> *do_dssp -s  topol.tpr  -f  t raj.xtc  -o  ss.xpm *
>>
>>
>> It selects "Protein" by it-self without any control from me. I want to
>> choose
>> from the list, for example not protein but C-alpha.
>>
>
> That shouldn't happen.  You should be prompted for a selection.  Note that
> selecting only C-alpha atoms will not work.  DSSP requires all MainChain
> atoms to be considered, since the secondary structure criteria are based on
> hydrogen bonding distances.  An incorrect selection could explain the error
> you get below.
>
> -Justin
>
>  To solve this probIem, I prepared the index file which includes only
>> C-alphas of
>> my system. Then, I use the following:
>> *do_dssp  -s  topol.tpr  -f   traj.xtc  -n   C_alpha.ndx*
>>
>>  I get the below fatal error:
>> Program do_dssp, VERSION 4.5.4
>> Source code file: do_dssp.c, line: 566
>> Fatal error:
>> Failed to execute command: /home_palamut2/mguler/dssp/**dsspcmbi -na
>> ddcblxTU
>> ddq8aNVV > /dev/null 2> /dev/null
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at 
>> http://www.gromacs.org/**Documentation/Errors
>> Are there any suggestions or corrections? Thanks in advance..
>> Turgay
>>
>>
>>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
> --
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Re: [gmx-users] N-terminus problem

[Emine Deniz Tekin]

Hi Mark,

Thank you for your reply.

Let me explain the problem a little more and answer your questions. I would
be happy if you could expound upon your reply.

  Hi Gromacs users,

I created a lipopeptide (lauroic acid  connected to an 8-residue peptide
> which starts with Valine).
>
> How is the link from acid to peptide created?
>
> The link between acid and peptide is a “peptide bond”.
>
> (I prepared the *rtp *entry for the lauroic acid make a peptide bond as if 
> lauroic acid was an amino acid (following your suggestion)).
>
>
>  If I try to use “pdb2gmx” for ONE LİPOPEPTİDE (9 residues), that is
>
>  pdb2gmx –f one_lipopeptide.pdb -ter
>
> It seems to work. That is, topol.top is created. (And also this topology
> works  for MD.)
>
>
>  Does that topology work for MD? Why does pdb2gmx think there's 9
> residues, and below there seem to be 63?
>
·  But, if I try to use “pdb2gmx” for SEVEN LİPOPEPTİDE at
desired positions (63 residues), that is

pdb2gmx –f seven_lipopeptide.pdb -ter
  It gives the fatal error: “Atom N not found in residue seq.nr. 1 while
adding improper”

> While I was creating the lipopeptide, I introduced the lauroic acid as a
> pseudo amino acid (following Mark’s suggestion). So, I really do NOT have
> atom N in the first residue. I pasted a part of my gro file below.
>
>  Some improper in your topology database entries wants a N atom that
> doesn't exist. Unfortunately, we don't have anywhere near enough information
> to guess why. pdb2gmx is trying to match your .rtp and specbond entries to
> your .gro file, but only seeing the latter can't help diagnose a mismatch.
> Some description of "desired positions" is also important.
>

I wrote  a code to put 7 identical lipopeptides at desired positions.
That is, 7 lipopeptides are placed on a plane with 15 degree angle between
the adjacent lipopeptides.


>
> Also, giving full command lines are always preferred. You may not think
> anything significant is there, and you might be right, but if there *can* be
> something significant there, and we aren't given the chance to know whether
> it is present, we might just not bother to waste time guessing :)
>

I used gromos53a6 force field (extended to include lauroic acid parameters)
& spc type water


>   And also, I have a question: The first residue in my pdb file is lauroic
acid that is DPP, second residue is Valine and so on.. But when I used the
pdb2gmx with –ter it says: Start terminus VAL-2: None, End terminus ASP-9:
COO-) Would not DPP residue be the start terminus?

Best regards,

Mark

> Deniz
>
>
>   GROMACS molecule input test
>
> 574
>
> 1DPP CA1  11.027   5.295   3.153
>
> 1DPP CB2  10.894   5.299   3.078
>
> 1DPP CG3  10.777   5.234   3.153
>
> 1DPP CD4  10.645   5.254   3.078
>
> 1DPP CE5  10.521   5.203   3.153
>
> 1DPP CZ6  10.392   5.251   3.086
>
> 1DPP CM7  10.266   5.207   3.161
>
> 1DPP CN8  10.140   5.272   3.103
>
> 1DPP CO9  10.014   5.221   3.172
>
> 1DPP CP   10   9.885   5.279   3.112
>
> 1DPP CQ   11   9.761   5.203   3.160
>
> 1DPP  C   12  11.101   5.430   3.147
>
> 1DPP  O   13  11.032   5.531   3.136
>
> 2VAL  N   14  11.235   5.450   3.160
>
> 2VAL  H   15  11.249   5.550   3.159
>
> 2VAL CA   16  11.368   5.385   3.181
>
> 2VAL CB   17  11.390   5.233   3.181
>
> 2VALCG1   18  11.332   5.172   3.308
>
> 2VALCG2   19  11.338   5.161   3.056
>
> 2VAL  C   20  11.486   5.449   3.103
>
> 2VAL  O   21  11.498   5.436   2.982
>
> ..
>
>63ASPOD1  570  -0.306  14.874   3.343
>
>63ASPOD2  571  -0.451  15.030   3.289
>
>63ASP  C  572  -0.057  15.023   3.106
>
>63ASP O1  573   0.014  15.003   3.207
>
>63ASP O2  574  -0.029  15.104   3.017
>
>   16.23937   16.23937   16.23937
>
>
>   I am using Gromacs 53a6 force field and gromacs 4.5.3 version.
>
> Any help will be appreciated.
>
>  Thanks in advance
>
>
>
> Deniz
>
>
>
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[gmx-users] N-terminus problem

[Emine Deniz Tekin]

Hi Gromacs users,


I created a lipopeptide (lauroic acid  connected to an 8-residue peptide
which starts with Valine).

· If I try to use pdb2gmx with -ter flag   (Start terminus VAL-2:
None, End terminus ASP-9: COO-), everything seems to work (topology is
created.).

· But, if I try to use pdb2gmx with -ter flag  for more than one
lipopeptide at desired positions, it gives the following error. (again says
Start terminus VAL-2: None, End terminus ASP-9: COO- )

 *Fatal error:  Atom N not found in residue seq.nr. 1 while adding improper*

While I was creating the lipopeptide, I introduced the lauroic acid as a
pseudo amino acid (following Mark’s suggestion). So, I really do NOT have
atom N in the first residue. I pasted a part of my gro file below.


GROMACS molecule input test

574

1DPP CA1  11.027   5.295   3.153

1DPP CB2  10.894   5.299   3.078

1DPP CG3  10.777   5.234   3.153

1DPP CD4  10.645   5.254   3.078

1DPP CE5  10.521   5.203   3.153

1DPP CZ6  10.392   5.251   3.086

1DPP CM7  10.266   5.207   3.161

1DPP CN8  10.140   5.272   3.103

1DPP CO9  10.014   5.221   3.172

1DPP CP   10   9.885   5.279   3.112

1DPP CQ   11   9.761   5.203   3.160

1DPP  C   12  11.101   5.430   3.147

1DPP  O   13  11.032   5.531   3.136

2VAL  N   14  11.235   5.450   3.160

2VAL  H   15  11.249   5.550   3.159

2VAL CA   16  11.368   5.385   3.181

2VAL CB   17  11.390   5.233   3.181

2VALCG1   18  11.332   5.172   3.308

2VALCG2   19  11.338   5.161   3.056

2VAL  C   20  11.486   5.449   3.103

2VAL  O   21  11.498   5.436   2.982

..

   63ASPOD1  570  -0.306  14.874   3.343

   63ASPOD2  571  -0.451  15.030   3.289

   63ASP  C  572  -0.057  15.023   3.106

   63ASP O1  573   0.014  15.003   3.207

   63ASP O2  574  -0.029  15.104   3.017

  16.23937   16.23937   16.23937


I am using Gromacs 53a6 force field and gromacs 4.5.3 version.

Any help will be appreciated.

 Thanks in advance



Deniz
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[gmx-users] Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms while sorting atoms.

[Emine Deniz Tekin]

Hi all,


I wrote a own code to put three identical lipopeptide at desired positions.
Then I used the pdb2gmx with –ter flag to get the system’s topology, I have
encountered the following error:


Fatal error:

Atom OXT in residue ASP 18 was not found in rtp entry ASP with 9 atoms

while sorting atoms.


But, I am sure that there is no such defined atom type (OXT) neither in “
.rtp” fıle nor “ .pdb” file.

And also, I searched the mailing-list. I found the following link but
still could not figure out the problem.

http://lists.gromacs.org/pipermail/gmx-users/2010-September/054209.html



(I am using gromos53a6 force field.)



Any help will be appreciated.



Thanks in advance



Deniz
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[gmx-users] strain

[Emine Deniz Tekin]

Hi Gromacs users,

We would like to apply strain to the system. Is this possible to do with
gromacs and if it is how?

Thank you in advance,

Deniz
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[gmx-users] gen-pairs

[Emine Deniz Tekin]

Hi gromacs users,


I wish to simulate a system using the Gromos53a6 force field.  When I try to
run, I get the following errors:


ERROR 1 [file topol.top, line 194]:  No default LJ-14 types

ERROR 2 [file topol.top, line 195]:  No default LJ-14 types

ERROR 3 [file topol.top, line 198]:  No default LJ-14 types

ERROR 4 [file topol.top, line 200]:  No default LJ-14 types

ERROR 5 [file topol.top, line 201]:  No default LJ-14 types

ERROR 6 [file topol.top, line 202]:  No default LJ-14 types

ERROR 7 [file topol.top, line 203]:  No default LJ-14 types



I checked which atom pairs are listed in the topol.top lines 194, 195, 198,
200-203. As far as I can understand, I haven’t properly given the atom types
in the [pairtypes] section in ffnonbonded.itp, therefore grompp gave me this
error. Then, I simply changed the “gen-pairs=NO”, to “gen-pairs=YES”, and it
seemed to work well.



[ defaults ]

; nbfunccomb-rule   gen-pairs   fudgeLJ fudgeQQ

1  1 yes 1.0 1.0


However, I  wonder if  this is OK or not ?

Thank you in advance,


Deniz
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Re: [gmx-users] aminoacids.n.tdb

[Emine Deniz Tekin]

Hi Mark,

Thanks again. Your suggestion of introducing the lauroic acid as a
pseudo-amino acid seems to solve my problem. Below is my corrected
"aminoacids.rtp" file for the 6-Carbon case as a test. (I used the Berger
lipid parameters.) Just to be sure, could you have a look at the file (I
used gb_10 between C and +N instead of gb_19).


[ DPP ]

 [ atoms ]

   CA   LP20.0   0

   CB   LP20.0   1

   CG   LP20.0   2

   CD   LP20.0   3

   CE   LP30.0   4

CLC  0.450   5

OLO -0.450  5

 [ bonds ]

   CACB 1   0.15300E+00 0.33470E+06

   C CA  1   0.15300E+00 0.33470E+06

   CBCG 1  0.15300E+00 0.33470E+06

   CGCD 1  0.15300E+00 0.33470E+06

   CDCE 1   0.15300E+00 0.33470E+06

C O   1   0.12300E+00 0.50210E+06

C+N  gb_10

[ angles ]

   C CACB  1  0.11100E+03 0.46020E+03

   CACBCG 1  0.11100E+03 0.46020E+03

   CBCGCD 1  0.11100E+03 0.46020E+03

   CGCDCE 1  0.11100E+03 0.46020E+03

   O  CCA   1  0.12100E+03 0.50210E+03

   CA C+N ga_19

O C+N ga_33

[ dihedrals ]

CCACBCG   10.0 5.863

 CACBCGCD 3

   CBCGCDCE   3

 [ impropers ]

CCA+N Ogi_1

Best regards,

Deniz

On Tue, Apr 12, 2011 at 4:26 PM, Mark Abraham wrote:

>  On 12/04/2011 10:30 PM, Emine Deniz Tekin wrote:
>
>
> Hi Mark,
>
>
> Thank you for your reply. But, I couldn’t understand very well what you
> meant “you can make one that uses backbone-style linking. Most of the
> forcefields will have examples of non-amino-acid terminating residues -
> these make a single peptide bond just like yours does.”. So, let me
> explain the problem a little more.  I would be happy if you could expound
> upon your reply.
>
>
>  *1)*  I prepared the *rtp *entry for the lauroic acid (see below) and
> add the lipid parameters to the relevant sections of the *ffnonbonded.itp*and
> *ffbonded.itp* files.
>
>
> That is not an .rtp entry, see below. Look at some .rtp entries and see how
> they make backbone bonds. That is what I understand you want to do - make a
> peptide bond as if lauroic acid was an amino acid.
>
>
>  *2)*  I added the lauroic acid as a "Non-Protein” in the *
> residuetypes.dat *file and also I introduced the atom types (LO: 15.9994,
> LC: 12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.*
>
> *3)  *I concatenated the structure files of a 8-residue-peptide* *and
> lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained the 
> *topol.top,
> conf.gro* and *posre.itp* for *the whole system.* (I chose : start
> terminus VAL-2: NH2 and end terminus ASP-9: COO-)
>
> *4)*   But when I looked into *conf.gro* with the VMD, I see that the
> peptide bond is formed between the
>
>
> No bond shown by VMD is relevant. It's guessing based on the coordinates in
> your .gro file. Your bonded atoms are in your .top file. VMD knows nothing
> about your .top file.
>
>
>  lauroic acid (C34) and the N terminal of the Valine. However, second H of
> the N is still there and it is making another bond with C34 of lauroic acid.
> The strange thing is: C34 is double bonded to O35, Carbon makes four
> bonds.
>
> How can I get rid of that H?
>
> [ DPP ]
>
>
> This is not an .rtp entry. The [bonds] section must refer to atom names. I
> can only suppose pdb2gmx is warning about or ignoring everything after your
> [atoms] section.
>
> Look in the .rtp and chapter 5 of the manual how terminating
> pseudo-residues like ACE work. Do something analogous for lauroic acid.
>
> Mark
>
>
>   [ atoms ]
>
>C34   LC 0.80018
>
>O35   LO-0.60 18
>
>C36  LP2  0   19
>
>C37  LP2  0   20
>
>C38  LP2  0   21
>
>C39  LP2  0   22
>
>C40  LP2  0   23
>
>C41  LP2  0   24
>
>C42  LP2  0   25
>
>C43  LP2  0   26
>
>C44  LP2  0   27
>
>C45  LP2  0   28
>
>C46  LP3  0   29
>
> [ bonds ]
>
> ;  aiaj funct
>
>   34  35   1 0.12300E+00 0.50210E+06
>
>   34  36   1 0.15300E+00 0.33470E+06
>
>   36  37   1 0.15300E+00 0.33470E+06
>
>   37  38   1 0.15300E+00 0.33470E+06
>
>   38  39   1 0.15300E+00 0.33470E+06
>
>   39  40   1 0.15300E+00 0.33470E+06
>
>   40  41   1 0.15300E+00 0.33

Re: [gmx-users] aminoacids.n.tdb

[Emine Deniz Tekin]

Hi Mark,


Thank you for your reply. But, I couldn’t understand very well what you
meant “you can make one that uses backbone-style linking. Most of the
forcefields will have examples of non-amino-acid terminating residues -
these make a single peptide bond just like yours does.”. So, let me explain
the problem a little more.  I would be happy if you could expound upon your
reply.


*1)*  I prepared the *rtp *entry for the lauroic acid (see below) and
add the lipid parameters to the relevant sections of the *ffnonbonded.itp*and
*ffbonded.itp* files.

*2)*  I added the lauroic acid as a "Non-Protein” in the *
residuetypes.dat *file and also I introduced the atom types (LO: 15.9994,
LC: 12.0110, LP2: 14.0270, LP3: 15.0350) in the *atomtypes.atp.*

*3)  *I concatenated the structure files of a 8-residue-peptide* *and
lauroic acid as *system.gro. *Then, using “pdb2gmx -ter”, I obtained
the *topol.top,
conf.gro* and *posre.itp* for *the whole system.* (I chose : start terminus
VAL-2: NH2 and end terminus ASP-9: COO-)

*4)*   But when I looked into *conf.gro* with the VMD, I see that the
peptide bond is formed between the lauroic acid (C34) and the N terminal of
the Valine. However, second H of the N is still there and it is making
another bond with C34 of lauroic acid. The strange thing is: C34 is double
bonded to O35, Carbon makes four bonds.

How can I get rid of that H?

[ DPP ]

 [ atoms ]

   C34   LC 0.80018

   O35   LO-0.60 18

   C36  LP2  0   19

   C37  LP2  0   20

   C38  LP2  0   21

   C39  LP2  0   22

   C40  LP2  0   23

   C41  LP2  0   24

   C42  LP2  0   25

   C43  LP2  0   26

   C44  LP2  0   27

   C45  LP2  0   28

   C46  LP3  0   29

[ bonds ]

;  aiaj funct

  34  35   1 0.12300E+00 0.50210E+06

  34  36   1 0.15300E+00 0.33470E+06

  36  37   1 0.15300E+00 0.33470E+06

  37  38   1 0.15300E+00 0.33470E+06

  38  39   1 0.15300E+00 0.33470E+06

  39  40   1 0.15300E+00 0.33470E+06

  40  41   1 0.15300E+00 0.33470E+06

  41  42   1 0.15300E+00 0.33470E+06

  42  43   1 0.15300E+00 0.33470E+06

  43  44   1 0.15300E+00 0.33470E+06

  44  45   1 0.15300E+00 0.33470E+06

  45  46   1 0.15300E+00 0.33470E+06

[ angles ]

;  aiajak funct

  34  36  37   1 0.11100E+03 0.46020E+03

  35  34  36   1 0.12100E+03 0.50210E+03

  36  37  38   1 0.11100E+03 0.46020E+03

  37  38  39   1 0.11100E+03 0.46020E+03

  38  39  40   1 0.11100E+03 0.46020E+03

  39  40  41   1 0.11100E+03 0.46020E+03

  40  41  42   1 0.11100E+03 0.46020E+03

  41  42  43   1 0.11100E+03 0.46020E+03

  42  43  44   1 0.11100E+03 0.46020E+03

  43  44  45   1 0.11100E+03 0.46020E+03

  44  45  46   1 0.11100E+03 0.46020E+03

[ dihedrals ]

;  aiajakal funct   phi0 cp mult

   34363738 10.0 5.863

   36373839 3

   37383940 3

   38394041 3

   39404142 3

   40414243 3

   41424344 3

   42434445 3

   43444546 3


Best regards,

Deniz




On Sun, Apr 10, 2011 at 3:02 AM, Mark Abraham wrote:

> On 8/04/2011 11:25 PM, Emine Deniz Tekin wrote:
>
>>
>> Hi Gromacs users,
>>
>> I want to covalently link the lauroic acid to the Valine residue (it is a
>> peptide (amide) bond), I know that I should update the specbond.dat.But
>> before updating this file, I need the NH as an N terminal of the first
>> residue (Valine).When I used pdb2gmx with the –ter flag, I got either NH3,
>> NH2 or None instead of NH.So, I add the [NH] directive in the
>> aminoacids.n.rtp file, as follows;
>>
>>
>> [ NH ]
>>
>> [ replace ]
>>
>> ; old-namenew-typenew-massnew-charge
>>
>> NLN14.0067-0.31
>>
>> CACH113.0190.127
>>
>> [ add ]
>>
>> 12HNCAC
>>
>> ;atom_typemasscharge
>>
>> H1.0080.31
>>
>> [ delete ]
>>
>> H
>>
>> [ bonds ]
>>
>> NHgb_2
>>
>> [ angles ]
>>
>> CANHga_11
>>
>> [ dihedrals ]
>>
>> HNCACgd_29
>>
>>
>>
>> (ps. I wrote the charges of N, CA and H according to values defined in
>> topol.top and also I used the Gromos96 53a6 force field)
>>
>>
>> Then, I used the pdb2gmx with –ter, I could see:
>>
>> Select start terminus type for VAL
>>

[gmx-users] aminoacids.n.tdb

[Emine Deniz Tekin]

Hi Gromacs users,

I want to covalently link the lauroic acid to the Valine residue (it is a
peptide (amide) bond), I know that I should update the specbond.dat.  But
before updating this file, I need the NH as an N terminal of the first
residue (Valine).  When I used  pdb2gmx with the –ter flag,  I got either
NH3, NH2 or None instead of NH. So, I add the [NH] directive in the
aminoacids.n.rtp file, as follows;


[ NH ]

[ replace ]

; old-name new-type new-mass  new-charge

 NLN14.0067   -0.31


CA   CH1 13.019  0.127

[ add ]

1   2   H   N   CA  C

;atom_type  mass   charge

H 1.008  0.31

[ delete ]

H

[ bonds ]

N   H  gb_2

[ angles ]

CA  N   H  ga_11

[ dihedrals ]

H  N   CA  C   gd_29

(ps. I wrote the charges of N, CA and H according to values defined in
topol.top and also I used the Gromos96 53a6 force field)


Then, I used the pdb2gmx with –ter, I could see:

Select start terminus type for VAL

 0: NH

 1: NH3+

 2: NH2

 3: None


Finally, I got the  topol.top, posre itp and conf.gro files. But when I
looked into conf.gro,  I see that I am getting  “None”.  How can I get the
NH ?


Thanks in advance for your help.



Best regards

Deniz
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Re: [gmx-users] lipopeptide problem

[Emine Deniz Tekin]

Hi Felix,
Thank you for your help.

Hi Justin,

I did not want to write a long e-mail describing what I did and what did not
work. All I wanted to learn was whether there was some more detailed
information somewhere that I can reach. You do not have to reply to an email
if you feel it is not worth it. Lecturing me on "willingness" is crossing
the line. How do you know how much I tried? Anyhow, thanks for your earlier
help, but you can simply skip my future postings.

Best regards,

Deniz


On Thu, Mar 17, 2011 at 12:00 AM, Justin A. Lemkul  wrote:

>
>
> Emine Deniz Tekin wrote:
>
>> Hi GROMACS Users,
>>
>> I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I
>> simulated a peptide before but this is the first time I am trying to combine
>> a lipid with a peptide (to get a lipo-peptide). I would be really happy if
>> you could help me out with the following question
>>
>> I am tring to create a louroic acid connected to and an 8-redidue peptide.
>> To create residues, I used ARGUSLAB . For the louric acid I used BERGER
>> lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined
>> ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the
>> topol.top files as described in the manual. But this procedure did not yet
>> give me an attached louric acid and peptide. I
>>
>
> Nor should you expect it to.  Building the parent force field does not give
> you a topology describing some molecular system.
>
>
> still have to play with the aminoacids.hdb, aminoacids.rtp,
>> residuetypes.dat, atomtypes.atp, and specbond.dat files. I would appreciate
>> if you could let me know how to modify these files, especially the
>> aminoacids.hdb file. I tried several things but it not
>>
>
> See the manual, section 5.6.4.  The contents and format are discussed at
> length.
>
>
> work. Note that, I applied the suggestions in
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
>> but it was not sufficient.
>>
>>
> If you want free help, you will have to do substantially better than "it
> was not sufficient."  What is not clear?  What have you tried and what was
> the result? If you want free help, you've got to demonstrate a willingness
> to do some work on your own.
>
> -Justin
>
> Best regards
>>
>> Deniz
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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[gmx-users] lipopeptide problem

[Emine Deniz Tekin]

Hi GROMACS Users,

I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I
simulated a peptide before but this is the first time I am trying to combine
a lipid with a peptide (to get a lipo-peptide). I would be really happy if
you could help me out with the following question

I am tring to create a louroic acid connected to and an 8-redidue peptide.
To create residues, I used ARGUSLAB . For the louric acid I used BERGER
lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined
ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the
topol.top files as described in the manual. But this procedure did not yet
give me an attached louric acid and peptide. I still have to play with the
aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and
specbond.dat files. I would appreciate if you could let me know how to
modify these files, especially the aminoacids.hdb file. I tried several
things but it not work. Note that, I applied the suggestions in
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field,
but it was not sufficient.

Best regards

Deniz
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[gmx-users] DENIZ-senin yapacagina benzer birsey yapmis, residue eklemis..

[Emine Deniz Tekin]

On Fri, Mar 4, 2011 at 9:13 AM, Mark Abraham wrote:

> On 3/03/2011 11:42 PM, Justin A. Lemkul wrote:
>
>>
>>
>> bharat gupta wrote:
>>
>>> The residue is a chromophore of Green Fluorescent Protein. The parameter
>>> file that I have got has the connection for serine and glycine :-
>>>
>>>
>> For those of us who aren't fluent in CHARMM (or whatever this is), it
>> would be more useful if you describe plainly the nature of the connection
>> between your chromophore and the protein.  If the bonds are simply between
>> backbone atoms (which should be the case for the GFP chromophore, right?)
>> then you specify the bonds within the .rtp file (making use of the +/-
>> connection feature), otherwise you have to use specbond.dat to build the
>> connections.
>>
>
> Agreed. However if things look anything like
> http://ca.wikipedia.org/wiki/Fitxer:The_chromophore_of_GFP.png then I'd
> make a single new residue for the whole chromophore and forget about
> specbond.dat. If you have to introduce new atom or interaction types, then
> you do that by analogy with the existing types, in consultation with chapter
> 5 of the manual and its CHARMM-equivalent.
>
> Mark
>
>
>>  !Connection to the ser fragment
>>> !--
>>> CT2  CT1  CP2c52.000   108. ! ALLOW   ALI PEP POL ARO
>>> HB   CT1  CP2c  50.000   109.5000 ! ALLOW  PEP
>>> NH1  CT1  CP2c  50.000   107. ! ALLOW   PEP POL ARO ALI
>>> NR2C CP2C CT1   40.00125.00   ! NR1C CP2C CT1   35.00121.40   ! !
>>>
>>> !Connection to the gly fragment
>>> !--
>>> NR1C CT2  C 50.000   107. NR1c CT2  HB 48.000   108.
>>> CP2C NR1C CT2   36.00129.00
>>> CP1C NR1C CT2   32.00123.40
>>>
>>>
>>> On Thu, Mar 3, 2011 at 1:23 AM, Mark Abraham 
>>> >> mark.abra...@anu.edu.au>> wrote:
>>>
>>>
>>>
>>>On 03/03/11, *bharat gupta * >>
>>> > wrote:
>>>
Hi,

I followed the tutorial
-
 http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Fieldfor
updating the Charmm FF for my modified residue ..

I added the residues to the .rtp file , then I added the new atom
types in .atp file ,
The compound has some linkage with serine and glycine ... I want
to know how and where shall I add the linkage parameters and the
parameters (in bits) given below

>>>
>>>Without some idea what you mean by "linkage with serine and glycine"
>>>it's too hard to offer help.
>>>
>>>Mark
>>>
>>>
>>>

(The parameter file of the compound looks like this ) ..
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb  b0
CA1  CA2   305.00  1.3750 !
CA2  CA3   305.00  1.3750 !
CA3  CA4   305.00  1.3750 !
HPc  CA1   340.000 1.08   !
HPc  CA2   340.000 1.08   !
HPc  CA3   340.000 1.08   !
HPc  CA4   340.000 1.08   !


ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types KthetaTheta0   Kub S0
!
NR2c CP2c NR1c  130.00114.00   ! CP2c NR2c CP1c  130.00
  106.00   ! CP2c NR1c CP1c  130.00107.90   ! NR2c CP1c CP1c
  130.00108.30   ! NR2c CP1c CE1c   45.80129.50   ! NR1c 
 CP1c
 OcH42.00126.00   !
NR1c CP1c CP1c  130.00103.00   !

!Connection to the ser fragment
!--
CT2  CT1  CP2c52.000   108. ! ALLOW   ALI PEP POL ARO
HB   CT1  CP2c  50.000   109.5000 ! ALLOW  PEP
NH1  CT1  CP2c  50.000   107. ! ALLOW   PEP POL ARO ALI
NR2C CP2C CT1   40.00125.00   !


!Connection to the gly fragment
!--
NR1C CT2  C 50.000   107. NR1c CT2  HB 48.000
 108.
CP2C NR1C CT2   36.00129.00
CP1C NR1C CT2   32.00123.40
!
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types Kchin   delta
!
CP2C NR2C CP1C CP1C14.  2   180.00 ! CP2C NR1C CP1C CP1C
14.  2   180.00 !
NR2C CP2C NR1C CP1C14.  2   180.00 !
NR2C CP1C CP1C NR1C 4.  2   180.00 ! NR1C CP2C NR2C CP1C
 4.  2   180.00 ! CA1  CA2  CA3  CA4  3.1000  2   180.00 !

!barrier CA-CB
CP1C CP1C CE1C HA1C 6.84   2   180.00 ! CP1C CP1C CE1C CA1
6.84   2   180.00 !
  

Re: [gmx-users] Residue 'DEF' not found in residue topology database

[Emine Deniz Tekin]

Hi Justin,


Thank you for your reply.


Before I contacted you and do what you suggested , I did the following way:
1)  Firstly, I created the lipopetide (12 Carbon atoms (tail) +
Val-Val-Ala-Gly-Glu-Arg-Gly-Asp) using ChemDraw and saved as a PDB. 2)
 Then,
I pasted my pdb file to the The Dundee PRODRG2.5 Server (beta) and I got
conf.gro and topol.top files. 3)  After completing some of the missing
information by hand at the topology file (e.g  #include
"gromos53a6.ff/forcefield.itp"..), started the simulation for 10 ns. Simulation
went through without an apparent error. But I saw that when I watch the
trajectory at Visual Molecular Dynamics (VMD), some bonds seem much longer
than they should be. What could be the reason for this? I wonder  if
something ‘s wrong in the above process.

Thank you in advance,



Deniz



On Wed, Feb 23, 2011 at 3:57 PM, Justin A. Lemkul  wrote:

>
>
> Emine Deniz Tekin wrote:
>
>>
>> Hi gromacs users,
>>
>>
>> I am using the gromacs 4.5.3 version. I created a lipopetide which consist
>> of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
>> (residues) using ARGUSLAB and I saved it as a pdb file.
>>
>> Then, when I used the following command in gromacs:
>>
>>  pdb2gmx   –flipopepArgus.pdb(GROMOS96 45a3 force field&spc type
>> water model)
>>
>>  I got the following error message:
>>
>>  Fatal error:
>>
>> Residue 'DEF' not found in residue topology database
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>>
>> website at http://www.gromacs.org/Documentation/Errors
>>
>>
>> As far as I could understand, there is no problem with the residues  but
>>  there is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen
>> atoms and an Oxygen atom, actually it is called a lauroic acid). These atoms
>> are defined as DEF.  I thought  I should  rename the pdb to the expected
>> name given in the .rtp file of  the 45a3 force field for my lipopeptide. But
>> I could not find a parameterization for the  lauroic acid. In this case,
>> what shoul I do?
>>
>>
>> At the
>> http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blockspage,
>>  I found;
>>
>>
>> *Abbrev.*
>>
>>
>>
>> *Source*
>>
>>
>>
>> *2*
>>
>>
>>
>> *Full Name*
>>
>>
>>
>> *Formula*
>>
>>
>>
>> *Specifics*
>>
>> LAU
>>
>>
>>
>> fa.itp
>>
>>
>>
>> O
>>
>>
>>
>> lauroic acid
>>
>>
>>
>> C_11 H_23 COOH
>>
>>
>>
>>
>> -
>>
>>
>> Does using fa.itp file solve my problem? If yes, where can I get this
>> file?
>>
>>
>>
> This topology is from the deprecated Gromos87 (hacked) force field called
> ffgmx.  Don't use it.  The reasons are described in the manual.  What's
> more, you can't use a standalone topology if your molecule is covalently
> linked to a peptide.  You can't have bonds between different [moleculetypes]
> (i.e. between topologies) in Gromacs.
>
> The proper procedure is to parameterize the lauroic acid:
>
> http://www.gromacs.org/Documentation/How-tos/Parameterization
>
> or obtain compatible parameters from elsewhere and implement them in your
> chosen force field:
>
>
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> You could use Berger lipid parameters for the lauroic acid moiety, you'll
> just have to add this residue to the force field.  The membrane protein
> tutorial I wrote will walk you through how to modify the force field
> properly.
>
> http://www.gromacs.org/Documentation/Tutorials#Membrane_Simulations
>
> -Justin
>
>
>  I would be so glad if you can help me solve this problem.
>> Thank you in advance,
>>
>> Deniz
>>
>>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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Re: [gmx-users] Website search broken

[Emine Deniz Tekin]

Hi Justin,

No matter what I search at gromacs search field, it gives the same error
message.
Deniz

On Wed, Feb 23, 2011 at 3:58 PM, Justin A. Lemkul  wrote:

>
> Hi,
>
> Is anyone else having problems using the search feature on the Gromacs
> site?  If I search for "tutorials," I get:
>
> Your advanced search query is not formatted properly, and thus was not
> understood by the search engine. Please consult our documentation on
> supported search operators.
> Table './gromacs_wikidb/query_log' is marked as crashed and should be
> repaired
> tutorials
>
> I know that this search should work, so I figured it was a robust test.
> Anything else I search for gives me an analogous result.
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
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>
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[gmx-users] Residue 'DEF' not found in residue topology database

[Emine Deniz Tekin]

Hi gromacs users,


I am using the gromacs 4.5.3 version. I created a lipopetide which consist
of 12 Carbon atoms (tail) connected to Val-Val-Ala-Gly-Glu-Arg-Gly-Asp
(residues) using ARGUSLAB and I saved it as a pdb file.

Then, when I used the following command in gromacs:

 pdb2gmx   –flipopepArgus.pdb(GROMOS96 45a3 force field&spc
type water model)

 I got the following error message:

 Fatal error:

Residue 'DEF' not found in residue topology database

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors



As far as I could understand, there is no problem with the residues  but  there
is a problem with the atoms in the tail (12 Carbon atoms, 23 Hydrogen atoms
and an Oxygen atom, actually it is called a lauroic acid). These atoms are
defined as DEF.  I thought  I should  rename the pdb to the expected name
given in the .rtp file of  the 45a3 force field for my lipopeptide. But I
could not find a parameterization for the  lauroic acid. In this case, what
shoul I do?


At the
http://www.gromacs.org/Documentation/File_Formats/Gromacs_Building_Blockspage,
I found;


  *Abbrev.*

*Source*

*2*

*Full Name*

*Formula*

*Specifics*

LAU

fa.itp

O

lauroic acid

C11H23COOH

-



Does using fa.itp file solve my problem? If yes, where can I get this file?


I would be so glad if you can help me solve this problem.
Thank you in advance,

Deniz
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