[gmx-users] Polyethylene Surface generation

2010-10-04 Thread Yash Gandhi 
Hi,
A few days ago I had posted a request regarding help with Polyethylene
surface generation. I had earlier taken help of an older thread to create a gmx
file for 
PE.
I also did the modifications in rtp and hdb files as mentioned in the link.
After a few thoughts I tried to create a pdb file using some logic. It's as
follows:

HETATM1  C1   EtB1  -4.243   0.027  -1.420
HETATM2  C2   EtB  1  -2.975  -0.719  -0.982
HETATM3  C1   Eth  2  -1.840   0.252  -0.620
HETATM4  C2   Eth  2  -0.566  -0.487  -0.180
HETATM5  C1   Eth  3   0.567   0.487   0.181
HETATM6  C2   Eth  3   1.841  -0.252   0.621
HETATM7  C1   EtE  4   2.976   0.719   0.983
HETATM8  C2   EtE  4   4.244  -0.026   1.420
HETATM9  H11  EtB  1  -5.058  -0.688  -1.680
HETATM   10  H12  EtB  1  -4.048   0.659  -2.317
HETATM   11  H13  EtB  1  -4.620   0.690  -0.609
HETATM   12  H21  EtB  1  -2.642  -1.393  -1.807
HETATM   13  H22  EtB  1  -3.213  -1.362  -0.102
HETATM   14  H11  Eth  2  -2.179   0.926   0.202
HETATM   15  H12  Eth  2  -1.609   0.895  -1.503
HETATM   16  H21  Eth  2  -0.227  -1.161  -1.003
HETATM   17  H22  Eth  2  -0.797  -1.130   0.702
HETATM   18  H11  Eth  3   0.228   1.161   1.003
HETATM   19  H12  Eth  3   0.798   1.129  -0.702
HETATM   20  H21  Eth  3   2.180  -0.926  -0.202
HETATM   21  H22  Eth  3   1.610  -0.895   1.504
HETATM   22  H11  EtE  4   2.643   1.393   1.807
HETATM   23  H12  EtE  4   3.213   1.362   0.102
HETATM   24  H21  EtE  4   5.059   0.688   1.679
HETATM   25  H22  EtE  4   4.621  -0.690   0.608
HETATM   26  H23  EtE  4   4.050  -0.658   2.317
CONECT12
CONECT213
CONECT324
CONECT43
END

after running pdb2gmx command and taking OPLSAA Force field with the
additional residues as mentioned in the link, I am getting the same error
always and I am not able to get the reason why
*
Fatal error:
Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
 while sorting atoms*

Please help me urgently as I am not able to know why is the EtOH residue
being used.

Thanking you
-- 
Yash Gandhi,
4th Year, BE (Hons) Chemical,
Birla Institute of Technology & Science, Pilani, India
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Polyethylene Surface generation

2010-10-04 Thread Mark Abraham 


- Original Message -
From: Yash Gandhi 
Date: Monday, October 4, 2010 20:32
Subject: [gmx-users] Polyethylene Surface generation
To: gmx-users@gromacs.org

> Hi,
> A few days ago I had posted a request regarding help with Polyethylene 
> surface generation. I had earlier taken help of an older thread to create a 
> gmx file for PE. I also did the modifications in rtp and hdb files as 
> mentioned in the link. After a few thoughts I tried to create a pdb file 
> using some logic. It's as follows:
 > 
> HETATM1  C1   EtB1  -4.243   0.027  -1.420 
> HETATM2  C2   EtB  1  -2.975  -0.719  -0.982 
> HETATM3  C1   Eth  2  -1.840   0.252  -0.620 
> HETATM4  C2   Eth  2  -0.566  -0.487  -0.180 
> HETATM5  C1   Eth  3   0.567   0.487   0.181 
> HETATM6  C2   Eth  3   1.841  -0.252   0.621 
> HETATM7  C1   EtE  4   2.976   0.719   0.983 
> HETATM8  C2   EtE  4   4.244  -0.026   1.420 
> HETATM9  H11  EtB  1  -5.058  -0.688  -1.680 
> HETATM   10  H12  EtB  1  -4.048   0.659  -2.317 
> HETATM   11  H13  EtB  1  -4.620   0.690  -0.609 
> HETATM   12  H21  EtB  1  -2.642  -1.393  -1.807 
> HETATM   13  H22  EtB  1  -3.213  -1.362  -0.102 
> HETATM   14  H11  Eth  2  -2.179   0.926   0.202 
> HETATM   15  H12  Eth  2  -1.609   0.895  -1.503 
> HETATM   16  H21  Eth  2  -0.227  -1.161  -1.003 
> HETATM   17  H22  Eth  2  -0.797  -1.130   0.702 
> HETATM   18  H11  Eth  3   0.228   1.161   1.003 
> HETATM   19  H12  Eth  3   0.798   1.129  -0.702 
> HETATM   20  H21  Eth  3   2.180  -0.926  -0.202 
> HETATM   21  H22  Eth  3   1.610  -0.895   1.504 
> HETATM   22  H11  EtE  4   2.643   1.393   1.807 
> HETATM   23  H12  EtE  4   3.213   1.362   0.102 
> HETATM   24  H21  EtE  4   5.059   0.688   1.679 
> HETATM   25  H22  EtE  4   4.621  -0.690   0.608 
> HETATM   26  H23  EtE  4   4.050  -0.658   2.317 
> CONECT12 
> CONECT213 
> CONECT324 
> CONECT43 
> END
> 
> after running pdb2gmx command and taking OPLSAA Force field with the 
> additional residues as mentioned in the link, I am getting the same error 
> always and I am not able to get the reason why
> 
> Fatal error:
>  Atom C1 in residue EtOH 1 not found in rtp entry with 9 atoms
>  while sorting atoms
> 
> Please help me urgently as I am not able to know why is the EtOH residue 
> being used.

EtOH for ethanol is defined in standard OPLS/AA force field files. pdb2gmx is 
trying to match what you've given it to that, rather than your ethylene .rtp 
entries. What are your .rtp entries? Have you got your PDB columns correct? 
Also, perhaps keeping atoms from the same residue adjacent will be a good idea.

Mark

-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Justin A. Lemkul 



Chansoo Kim wrote:

Dear Justin:


Please call me, 'chance'. 
I have been doing neutron scattering and MD on water. 
Thank you again for this conversation with you, Justin.


Right now, I am trying to do polymer simulation to mimic an interaction 
with a plasma.

To do so, I am targeting PE system.

Related to the my question related to the [Error] and [Question #1],

 [Error]
 When I did run the pdb2gmx, I got the following error.
 "Atom -C2 not found in residue PEth1 while adding hydrogens"



You can't specify a previous residue (designated by -) from the first residue in 
a chain.  Hence why I suggested what I did before about special terminal 
residues.  See the post I just sent about functioning .rtp and .hdb entries, 
they worked for me.


-Justin


 [Question #1]
 Therefore, what I should define more...?

I cannot avoid to ask you this question again!

As I emailed you, since I corrected error related to "blank" in the 
input files (pdb and etc.), it has never given me "segmentation fault."

The only error that the gromacs gives me is the above one.

Even though I am following your suggestion in the previous email, I want 
to clarify the above problem.


Do you have any idea on this...?

Thank you again!!


Sincerely yours,

Chance


(PS) The "chemical reaction", which I wrote in the second email, is my 
mistake. I did not mean "chemical reaction"... And I appreciate that you 
pointed it out.




On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul > wrote:




Chansoo Kim wrote:

Dear Justin:


Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..)
work, but I do not clearly understand chemical reaction, which I
have to define in those files...


No chemical reactions occur :)  See comments embedded below



[Situation]
I want to do simulate polyethylene (PE) using Gromacs and
OPLS-AA force field...

[Topology files and etc]
 (1) rtp file

[ Eth ]
 [ atoms ]
  C1opls_136-0.1201
  H11   opls_140 0.0601
  H12   opls_140 0.0601
  C2opls_136-0.1202
  H21   opls_140 0.0602
  H22   opls_140 0.0602
 [ bonds ]
  C1H11
  C1H12
  C1C2
  C2H21
  C2H22
  C2+C1


 (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


 (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
opls_140   1.008   0.06
[ delete ]
H21
H22


 (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
opls_140   1.008   0.06
[ delete ]
H21
H22


Note that the message you referenced in your first post (which
provided you with this .rtp entry) resulted in a segmentation fault,
therefore indicating that it probably won't work.



  (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


+ means next residue, - means previous.




[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my
terminal did NOT work...).
And those positions are all (0, 0, 0).


Right, because H positioning in a polymer chain may depend on
previous (-) or subsequent (+) residues, so the code doesn't know
where to put them.


Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Justin A. Lemkul 


I took a few minutes to look into this.  Since I have seen these same, 
incomplete posts that give no solution, let me propose one.  I was able to 
produce an OPLS-AA PE topology with pdb2gmx using the following additions to the 
corresponding .rtp and .hdb files:


ffoplsaa.rtp:

; Polyethylene - this is an internal residue
[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1

; Terminal PE residue ("beginning" of chain)
; designation arbitrary, C1 is -CH3
[ EthB ]
 [ atoms ]
   C1opls_135-0.1801
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   H13   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1H13
   C1C2
   C2H21
   C2H22
   C2+C1

; Terminal PE residue ("end" of chain)
; designation arbitrary, C2 is -CH3
[ EthE ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_135-0.1802
   H21   opls_140 0.0602
   H22   opls_140 0.0602
   H23   opls_140 0.0602
 [ bonds ]
   C1-C2
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2H23

ffoplsaa.hdb:

Eth 2
2   6   H1  C1  C2  -C2
2   6   H2  C2  C1  +C1
EthB2
3   4   H1  C1  C2  +C1
2   6   H2  C2  C1  +C1
EthE2
2   6   H1  C1  C2  -C2
3   4   H2  C2  C1  -C2 

I successfully created a topology from pdb2gmx using this .pdb file:

ATOM  1  C1  EthB1   1.000   1.540   0.000
ATOM  2  C2  EthB1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  EthE3   3.912   5.623   0.000
ATOM  6  C2  EthE3   5.368   6.124   0.000
END

I think the main reason the -n.tdb and -c.tdb modifications do not work is the 
following message from pdb2gmx: "No N- or C-terminus found: this chain appears 
to contain no protein."


I do not vouch for the validity of these parameters, as I have no need to test 
them.  This information is only meant to be instructive regarding using pdb2gmx 
to generate a topology; it is an exercise for the user to determine whether or 
not such parameters are valid.


-Justin

Zuzana Benkova wrote:

Dear Chansoo Kim,

It has passed relatively long time since I attempted to use pdb2gmx to 
build my topology for polyethylene. I prepared the relevant files 
according to those used for amino acids. I used + and – sign to discern 
the direction of connectivity. I have encountered dome problems 
mentioned in the mail but they have not been answered satisfactorily. 
Later on I wanted to run just united atom simulations and I had next 
problem with pdb2gmx that always include hydrogen atoms to my topology 
though I used option which should have disabled this. I decided to build 
my topology file without pdb2gmx and I applied force field that is not 
present in GMX directories.


 




*From:* gmx-users-boun...@gromacs.org 
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Chansoo Kim

*Sent:* Tuesday, March 03, 2009 2:50 PM
*To:* jalem...@vt.edu; Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - 
please!


 


Dear Justin:

 

 


Thank you for your reply.

I was too urgent, so I did not clarify my questions.

Sorry about that.

 

I totally understand how topology files (tdb, hdb, and etc..) work, but 
I do not clearly understand chemical reaction, which I have to define in 
those files...


 

 


*[Situation]*

I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force 
field...


 


*[Topology files and etc]*

  (1) rtp file

[ Eth ]

 [ atoms ]

   C1opls_136-0.1201

   H11   opls_140 0.0601

   H12   opls_140 0.0601

   C2opls_136-0.1202

   H21   opls_140 0.0602

   H22   opls_140 0.0602

 [ bonds ]

   C1H11

   C1H12

   C1C2

   C2H21

   C2H22

   C2+C1

 


  (2) hdb file

Eth 2

2   6   H1   C1  C2 +C1

2   6   H2   C2  C1 -C2

 

 


  (3) -c.tdb file

 


[ Eth ]

[ replace ]

C1  opls_13512.011  -0.18

[ add ]

34  H1  C1  C2

 opls_140   1.008   0.06

[ delete ]

H21

H22

 

 


  (4) -n.tdb file

 


[ Eth ]

[ replace ]

C2  opls_13512.011   -0.18

[ add ]

3

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Chansoo Kim 
Dear Justin and gmx-users:

Thank you for your answer, Justin.

Since I corrected error related to "blank" in the input files (pdb and
etc.), it has never given me "segmentation fault."
So... this problem is not related to this one anyway.

Now, I will try to correct others by following your suggestion.

After trying, I will contact you again... :)

Thank you again!!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 9:09 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Justin:
>>
>>
>> Thank you for your reply.
>> I was too urgent, so I did not clarify my questions.
>> Sorry about that.
>>
>> I totally understand how topology files (tdb, hdb, and etc..) work, but I
>> do not clearly understand chemical reaction, which I have to define in those
>> files...
>>
>>
> No chemical reactions occur :)  See comments embedded below
>
>
>
>> [Situation]
>> I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
>> field...
>>
>> [Topology files and etc]
>>  (1) rtp file
>>
>> [ Eth ]
>>  [ atoms ]
>>   C1opls_136-0.1201
>>   H11   opls_140 0.0601
>>   H12   opls_140 0.0601
>>   C2opls_136-0.1202
>>   H21   opls_140 0.0602
>>   H22   opls_140 0.0602
>>  [ bonds ]
>>   C1H11
>>   C1H12
>>   C1C2
>>   C2H21
>>   C2H22
>>   C2+C1
>>
>>
>>  (2) hdb file
>> Eth 2
>> 2   6   H1   C1  C2 +C1
>> 2   6   H2   C2  C1 -C2
>>
>>
>>  (3) -c.tdb file
>>
>> [ Eth ]
>> [ replace ]
>> C1  opls_13512.011  -0.18
>> [ add ]
>> 34  H1  C1  C2
>> opls_140   1.008   0.06
>> [ delete ]
>> H21
>> H22
>>
>>
>>  (4) -n.tdb file
>>
>> [ Eth ]
>> [ replace ]
>> C2  opls_13512.011   -0.18
>> [ add ]
>> 34  H2  C2  C1
>> opls_140   1.008   0.06
>> [ delete ]
>> H21
>> H22
>>
>>
> Note that the message you referenced in your first post (which provided you
> with this .rtp entry) resulted in a segmentation fault, therefore indicating
> that it probably won't work.
>
>
>>   (5) input pdb file
>>
>> ATOM 1 C1 Eth 1 1.000 1.540 0.000
>>
>> ATOM  2  C2  Eth 1   2.456   2.041   0.000
>> ATOM  3  C1  Eth 2   2.456   3.581   0.000
>> ATOM  4  C2  Eth 2   3.912   4.083   0.000
>> ATOM  5  C1  Eth 3   3.912   5.623   0.000
>> ATOM  6  C2  Eth 3   5.368   6.124   0.000
>> END
>>
>>
>> [Error]
>> When I did run the pdb2gmx, I got the following error.
>> "Atom -C not found in residue PEth1 while adding hydrogens"
>>
>> [Question #1 and #2]
>> Therefore, what I should define more...?
>> What does the "+" and "-" mean here?
>>
>
> + means next residue, - means previous.
>
>
>>
>> [If...]
>> If I change the hdb file as follows,
>>
>> Eth 2
>> 2   6   H1   C1  C2 C1
>> 2   6   H2   C2  C1 C2
>>
>>
>> After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did
>> NOT work...).
>> And those positions are all (0, 0, 0).
>>
>>
> Right, because H positioning in a polymer chain may depend on previous (-)
> or subsequent (+) residues, so the code doesn't know where to put them.
>
>
>  Following is the results,
>>
>> LE Giving Russians Opium May Alter Current Situation
>> MODEL1
>> ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
>> ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
>> ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
>> ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
>> ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
>> ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
>> ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
>> ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
>> ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
>> ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
>> TER
>> ENDMDL
>>
>> [Question #3 from If... section ]
>> I guess that I have to change hdb and tdb files.
>> Would you please give some guide on that...?
>>
>>
> Knowing that many people have tried to define PE with .tdb entries (and I
> think success is limited), I would suggest the following.  Define distinct
> .rtp entries for the caps of your chain.  Don't bother with -n.tdb and
> -c.tdb; I d

RE: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Zuzana Benkova 
Dear Chansoo Kim,

It has passed relatively long time since I attempted to use pdb2gmx to build
my topology for polyethylene. I prepared the relevant files according to
those used for amino acids. I used + and - sign to discern the direction of
connectivity. I have encountered dome problems mentioned in the mail but
they have not been answered satisfactorily. Later on I wanted to run just
united atom simulations and I had next problem with pdb2gmx that always
include hydrogen atoms to my topology though I used option which should have
disabled this. I decided to build my topology file without pdb2gmx and I
applied force field that is not present in GMX directories. 

 

  _  

From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Chansoo Kim
Sent: Tuesday, March 03, 2009 2:50 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

 

Dear Justin:

 

 

Thank you for your reply.

I was too urgent, so I did not clarify my questions.

Sorry about that.

 

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...

 

 

[Situation]

I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

 

[Topology files and etc]

  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1
 
  (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2

 

 
  (3) -c.tdb file
 
[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22

 

 
  (4) -n.tdb file
 
[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22

 

   (5) input pdb file

 

ATOM  1  C1  Eth 1   1.000   1.540   0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END

 

[Error]

When I did run the pdb2gmx, I got the following error.

"Atom -C not found in residue PEth1 while adding hydrogens"

 

[Question #1 and #2]

Therefore, what I should define more...?

What does the "+" and "-" mean here?

 

 

[If...]

If I change the hdb file as follows,

 

 
Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2

 

After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).

And those positions are all (0, 0, 0).

 

Following is the results,

 

LE Giving Russians Opium May Alter Current Situation

MODEL1

ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00

ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00

ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00

ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00

ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00

ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00

ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00

ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00

ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00

ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00

TER

ENDMDL

 

[Question #3 from If... section ]

I guess that I have to change hdb and tdb files.

Would you please give some guide on that...?

 

Thank you for your care!

 

 

Sincerely yours,

 

C Kim

 

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:



Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Justin A. Lemkul 



Chansoo Kim wrote:

Dear Justin:


Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but 
I do not clearly understand chemical reaction, which I have to define in 
those files...




No chemical reactions occur :)  See comments embedded below



[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force 
field...


[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb file
Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22



Note that the message you referenced in your first post (which provided you with 
this .rtp entry) resulted in a segmentation fault, therefore indicating that it 
probably won't work.




   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


+ means next residue, - means previous.




[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did 
NOT work...).

And those positions are all (0, 0, 0).



Right, because H positioning in a polymer chain may depend on previous (-) or 
subsequent (+) residues, so the code doesn't know where to put them.



Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?



Knowing that many people have tried to define PE with .tdb entries (and I think 
success is limited), I would suggest the following.  Define distinct .rtp 
entries for the caps of your chain.  Don't bother with -n.tdb and -c.tdb; I 
don't know how well the Gromacs code handles non-protein termini (maybe it 
works, but it seems to give fits for polymers).  The .rtp entry for PE you've 
shown above seems reasonable enough for a PE monomer within the chain, but may 
require some tweaking (since I've never tried, I don't know).


-Justin


Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul > wrote:




Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it
could be not that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users
mailing list to tackle my problems.

[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Chansoo Kim 
Oops...I am truly sorry to bother your mailbox again...
Please understand this beginner...

Error message was, ""Atom -C2 not found in residue PEth1 while adding
hydrogens"

-- Forwarded message --
From: Chansoo Kim 
Date: Tue, Mar 3, 2009 at 8:49 AM
Subject: Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!
To: jalem...@vt.edu, Discussion list for GROMACS users <
gmx-users@gromacs.org>


Dear Justin:

Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...


[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb fileEth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22


   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).
And those positions are all (0, 0, 0).

Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?

Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Dr. Benkova and others:
>>
>>
>> I am C. Kim and trying to simulation polymer system.
>>
>> Since I guessed that polyethylene (PE) is a simple system, it could be not
>> that hard to simulate it in Gromacs.
>> Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
>> to tackle my problems.
>> Sorry to say, I could not solve problems, so I am asking your help!
>>
>> Actually I have used your files written in followings,
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
>>
>> [Q1]
>> After getting the result from the pdb2gmx, I could not see any H-atoms in
>> my system.
>> All the H-atoms have 0, 0, 0 positions!
>> Therefore, my question is
>>   how I should define hdb?
>>
>
> The .hdb file format is explai

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Chansoo Kim 
Dear Justin:

Thank you for your reply.
I was too urgent, so I did not clarify my questions.
Sorry about that.

I totally understand how topology files (tdb, hdb, and etc..) work, but I do
not clearly understand chemical reaction, which I have to define in those
files...


[Situation]
I want to do simulate polyethylene (PE) using Gromacs and OPLS-AA force
field...

[Topology files and etc]
  (1) rtp file

[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1


  (2) hdb fileEth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2


  (3) -c.tdb file

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


  (4) -n.tdb file

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22


   (5) input pdb file

ATOM 1 C1 Eth 1 1.000 1.540 0.000

ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END


[Error]
When I did run the pdb2gmx, I got the following error.
"Atom -C not found in residue PEth1 while adding hydrogens"

[Question #1 and #2]
Therefore, what I should define more...?
What does the "+" and "-" mean here?


[If...]
If I change the hdb file as follows,

Eth 2
2   6   H1   C1  C2 C1
2   6   H2   C2  C1 C2


After doing pdb2gmx, I got only 12 H-atoms (which means my terminal did NOT
work...).
And those positions are all (0, 0, 0).

Following is the results,

LE Giving Russians Opium May Alter Current Situation
MODEL1
ATOM  1  C1  PEt 1   1.000   0.000   0.000  1.00  0.00
ATOM  2  H11 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  3  H12 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  4  C2  PEt 1   2.450   6.000   1.000  1.00  0.00
ATOM  5  H21 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  6  H22 PEt 1   0.000   0.000   0.000  1.00  0.00
ATOM  7  C1  PEt 2   2.450   6.000   1.000  1.00  0.00
ATOM  8  H11 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM  9  H12 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 10  C2  PEt 2   3.910   2.000   3.000  1.00  0.00
ATOM 11  H21 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 12  H22 PEt 2   0.000   0.000   0.000  1.00  0.00
ATOM 13  C1  PEt 3   3.910   2.000   3.000  1.00  0.00
ATOM 14  H11 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 15  H12 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 16  C2  PEt 3   5.360   8.000   4.000  1.00  0.00
ATOM 17  H21 PEt 3   0.000   0.000   0.000  1.00  0.00
ATOM 18  H22 PEt 3   0.000   0.000   0.000  1.00  0.00
TER
ENDMDL

[Question #3 from If... section ]
I guess that I have to change hdb and tdb files.
Would you please give some guide on that...?

Thank you for your care!


Sincerely yours,

C Kim

On Tue, Mar 3, 2009 at 8:35 AM, Justin A. Lemkul  wrote:

>
>
> Chansoo Kim wrote:
>
>> Dear Dr. Benkova and others:
>>
>>
>> I am C. Kim and trying to simulation polymer system.
>>
>> Since I guessed that polyethylene (PE) is a simple system, it could be not
>> that hard to simulate it in Gromacs.
>> Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
>> to tackle my problems.
>> Sorry to say, I could not solve problems, so I am asking your help!
>>
>> Actually I have used your files written in followings,
>>
>> http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html
>>
>> [Q1]
>> After getting the result from the pdb2gmx, I could not see any H-atoms in
>> my system.
>> All the H-atoms have 0, 0, 0 positions!
>> Therefore, my question is
>>   how I should define hdb?
>>
>
> The .hdb file format is explained in the manual.
>
>
>> [Q2]
>> When I use -C2, and +C1 in hdb file, I always meet error.
>>
>
> What is the error?
>
> -Justin
>
>  Is there any other things to add to the ffopls*.* files...?
>>
>> Thank you for your care!
>>
>>
>> Sincerely
>> C. Kim
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list.

Re: [gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Justin A. Lemkul 



Chansoo Kim wrote:

Dear Dr. Benkova and others:


I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be 
not that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing 
list to tackle my problems.

Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms 
in my system.

All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
   how I should define hdb?


The .hdb file format is explained in the manual.



[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.


What is the error?

-Justin


Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely 


C. Kim




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php


--


Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
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://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Polyethylene (PE) simulations in Gromacs - please!

2009-03-03 Thread Chansoo Kim 
Dear Dr. Benkova and others:

I am C. Kim and trying to simulation polymer system.

Since I guessed that polyethylene (PE) is a simple system, it could be not
that hard to simulate it in Gromacs.
Trying to do, I have read Dr. Benkova's articles in gmx-users mailing list
to tackle my problems.
Sorry to say, I could not solve problems, so I am asking your help!

Actually I have used your files written in followings,

http://www.mail-archive.com/gmx-users@gromacs.org/msg12204.html

[Q1]
After getting the result from the pdb2gmx, I could not see any H-atoms in my
system.
All the H-atoms have 0, 0, 0 positions!
Therefore, my question is
   how I should define hdb?

[Q2]
When I use -C2, and +C1 in hdb file, I always meet error.
Is there any other things to add to the ffopls*.* files...?

Thank you for your care!


Sincerely

C. Kim
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Polyethylene

2008-02-18 Thread Zuzana Benkova 

Dear GMX users,
I want to prepare .gro and topology file starting from the .pdb file  
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.  
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as  
follows


[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1
 In ffoplsaa.hdb I defined it as

Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2

At this point I have to note that the presence of the last control  
atoms in this file has not influenced the process.

In ffoplsaa-n.tdb file I have added

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22

and in ffoplsaa-c.tdb file I have added

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H21
H22


After using pdb2gmx -f input.pdb I have obtained following message

Opening library file ffoplsaa.rtp
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat

Reading hexane.pdb...
Read 6 atoms
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat

26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 6 atoms
  chain  #res #atoms
  1 ' ' 3  6
All occupancies are one
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp

Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 59
Sorting it all out...
Opening library file ffoplsaa.hdb
Error in hdb file: nah = 41
line = ''
Opening library file ffoplsaa-n.tdb
Opening library file ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (6 atoms, 3 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat

5 out of 5 lines of specbond.dat converted succesfully
N-terminus: Eth
C-terminus: Eth
Segmentation fault

Could you specify what means Error in hdb file: nah = 41
line = '' and what is the problem with segmentation.

My input structure in .pdb file is as follows

ATOM  1  C1  Eth 1   1.000   1.540   0.000
ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END

Thank you for help in advance
Best regards
Zuzana


___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

[gmx-users] Polyethylene

2008-02-17 Thread Zuzana Benkova 

Dear GMX users,
I want to prepare .gro and topology files starting from the .pdb file  
for a polyethylene chain , whose residue is not defined in .rtp, .hdb.  
and .tdb files. I have defined a new residue in ffoplsaa.rtp file as  
follows


[ Eth ]
 [ atoms ]
   C1opls_136-0.1201
   H11   opls_140 0.0601
   H12   opls_140 0.0601
   C2opls_136-0.1202
   H21   opls_140 0.0602
   H22   opls_140 0.0602
 [ bonds ]
   C1H11
   C1H12
   C1C2
   C2H21
   C2H22
   C2+C1
 In ffoplsaa.hdb I defined it as

Eth 2
2   6   H1   C1  C2 +C1
2   6   H2   C2  C1 -C2

At this point I have to note that the presence of the last control  
atoms in this file has not influenced the process.

In ffoplsaa-n.tdb file I have added

[ Eth ]
[ replace ]
C2  opls_13512.011   -0.18
[ add ]
34  H2  C2  C1
 opls_140   1.008   0.06
[ delete ]
H21
H22

and in ffoplsaa-c.tdb file I have added

[ Eth ]
[ replace ]
C1  opls_13512.011  -0.18
[ add ]
34  H1  C1  C2
 opls_140   1.008   0.06
[ delete ]
H11
H12

After using pdb2gmx -f input.pdb I have obtained following message

Opening library file ffoplsaa.rtp
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/aminoacids.dat

Reading hexane.pdb...
Read 6 atoms
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/xlateat.dat

26 out of 26 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 3 residues with 6 atoms
  chain  #res #atoms
  1 ' ' 3  6
All occupancies are one
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/ffoplsaa.atp

Atomtype 817
Reading residue database... (ffoplsaa)
Opening library file ffoplsaa.rtp
Residue 59
Sorting it all out...
Opening library file ffoplsaa.hdb
Error in hdb file: nah = 41
line = ''
Opening library file ffoplsaa-n.tdb
Opening library file ffoplsaa-c.tdb
Back Off! I just backed up topol.top to ./#topol.top.8#
Processing chain 1 (6 atoms, 3 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Checking for duplicate atoms
Opening library file  
/usr/local/share/gromacs/gromacs-3.3/share/top/specbond.dat

5 out of 5 lines of specbond.dat converted succesfully
N-terminus: Eth
C-terminus: Eth
Segmentation fault

Could you specify what means Error in hdb file: nah = 41
line = '' and what is the problem with segmentation.

My input structure in .pdb file is as follows

ATOM  1  C1  Eth 1   1.000   1.540   0.000
ATOM  2  C2  Eth 1   2.456   2.041   0.000
ATOM  3  C1  Eth 2   2.456   3.581   0.000
ATOM  4  C2  Eth 2   3.912   4.083   0.000
ATOM  5  C1  Eth 3   3.912   5.623   0.000
ATOM  6  C2  Eth 3   5.368   6.124   0.000
END

Thank you for help in advance
Best regards
Zuzana

___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php