date:20130922

Re: [gmx-users] Re: No such moleculetype SOL

2013-09-22 Thread Justin Lemkul




On 9/22/13 10:10 PM, Jonathan Saboury wrote:

Then something is wrong with the way you've done it, because the job of

spc.itp

is to define the [moleculetype] SOL and all its relevant parameters.


Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by acpype. Still getting the error "Fatal error: No such
moleculetype SOL"

Here is a list of commands and explanations of what I did:
http://pastebin.com/raw.php?i=V5wrRdme
Here is the .top: http://pastebin.com/raw.php?i=LzCANQZw
Here are the files I am using: http://www.sendspace.com/file/5ps0i1



I should have seen this before.  The default spc.itp is not compatible with 
AMBER.  Have a look at the actual contents of spc.itp:


; This file is for backward compatibility only.
; Please directly include the spc.itp file from your force field directory.
#ifdef _FF_GROMACS
#include "gmx.ff/spc.itp"
#endif
#ifdef _FF_GROMOS96
#include "gromos43a1.ff/spc.itp"
#endif
#ifdef _FF_OPLS
#include "oplsaa.ff/spc.itp"
#endif

That said, there is an spc.itp within the AMBER subdirectories that needs to be 
#included more explicitly, i.e. #include "amber99sb.ff/spc.itp"


May I ask why you are using SPC?  The AMBER force fields were parametrized with 
TIP3P, so I see no viable reason to use a different water model.



It is important to note that genbox did not add the amount of cyclohexanes
added to system in the .top (it did do it for the waters though). Perhaps
that is a bug?



It's not a bug, because genbox does not advertise such a feature.  genbox is 
hard-coded to only ever deal with water.  Anything else is up to the user.



You need a parent force field that defines all the bonded and nonbonded
interactions in the system.  Whether or not this is one that comes with

Gromacs

or one you design yourself, you still have to satisfy all of the internal
mechanics (see Chapter 5).  Whether or not there is a protein is completely
irrelevant; force fields do much more than just proteins.


I see, interesting. Added it to the .top :)


Well, PRODRG parameters are pretty low-quality anyway, but it's a

convenient

example for doing a tutorial rather than trying to teach people how to use

other

external software ;)


As you know I am using acpype, is it any better? What do you use?



Any force field can be parametrized to give correct target data, especially for 
a molecule as simple as cyclohexane.  What I use is a complex question, because 
it depends entirely upon the task at hand :)


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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[gmx-users] Re: No such moleculetype SOL

2013-09-22 Thread Jonathan Saboury

>Then something is wrong with the way you've done it, because the job of
spc.itp
>is to define the [moleculetype] SOL and all its relevant parameters.

Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by acpype. Still getting the error "Fatal error: No such
moleculetype SOL"

Here is a list of commands and explanations of what I did:
http://pastebin.com/raw.php?i=V5wrRdme
Here is the .top: http://pastebin.com/raw.php?i=LzCANQZw
Here are the files I am using: http://www.sendspace.com/file/5ps0i1

It is important to note that genbox did not add the amount of cyclohexanes
added to system in the .top (it did do it for the waters though). Perhaps
that is a bug?

>You need a parent force field that defines all the bonded and nonbonded
>interactions in the system.  Whether or not this is one that comes with
Gromacs
>or one you design yourself, you still have to satisfy all of the internal
>mechanics (see Chapter 5).  Whether or not there is a protein is completely
>irrelevant; force fields do much more than just proteins.

I see, interesting. Added it to the .top :)

>Well, PRODRG parameters are pretty low-quality anyway, but it's a
convenient
>example for doing a tutorial rather than trying to teach people how to use
other
>external software ;)

As you know I am using acpype, is it any better? What do you use?

Thank you for the help Justin, it is extremely appreciated :)
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Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Justin Lemkul




On 9/22/13 9:32 PM, Nilesh Dhumal wrote:

Thanks.

I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.

How can I define for 128 EMI and 128 ETS ?



List 128 EMI consecutively, followed by 128 ETS consecutively, and make a 
[molecules] directive analogously.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Nilesh Dhumal

Thanks.

I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.

How can I define for 128 EMI and 128 ETS ?

Nilesh
>
> On 9/22/13 9:18 PM, Nilesh Dhumal wrote:
>> Sorry to paste big files here. (.pdb file and processed.top )
>>
>>
>> pdb file.
>>
>> TITLE Protein
>> REMARKTHIS IS A SIMULATION BOX
>> CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
>> MODEL1
>> ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
>> ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
>> ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
>> ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
>> ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
>> ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
>> ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
>> ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
>> ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
>> ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
>> ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
>> ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
>> ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
>> ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
>> ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
>> ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
>> ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
>> ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
>> ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
>> ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
>> ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
>> ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
>> ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
>> ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
>> ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
>> ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
>> ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
>> ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
>> ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
>> ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
>> ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
>> ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
>> ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00
>> ATOM 34  N3  EMI 3  25.074  30.288   7.940  1.00  0.00
>> ATOM 35  C4  EMI 3  26.335  30.336   7.464  1.00  0.00
>> ATOM 36  N5  EMI 3  26.369  29.867   6.216  1.00  0.00
>> ATOM 37  C6  EMI 3  27.586  29.761   5.460  1.00  0.00
>> ATOM 38  C7  EMI 3  27.397  29.088   4.106  1.00  0.00
>> ATOM 39  C8  EMI 3  24.601  30.404   9.351  1.00  0.00
>> ATOM 40  H9  EMI 3  24.815  29.446   4.790  1.00  0.00
>> ATOM 41  H10 EMI 3  23.203  29.817   6.920  1.00  0.00
>> ATOM 42  H11 EMI 3  27.238  30.558   8.074  1.00  0.00
>> ATOM 43  H12 EMI 3  24.321  29.435   9.759  1.00  0.00
>> ATOM 44  H13 EMI 3  25.411  30.876   9.880  1.00  0.00
>> ATOM 45  H14 EMI 3  23.735  31.092   9.515  1.00  0.00
>> ATOM 46  H15 EMI 3  28.216  29.130   6.169  1.00  0.00
>> ATOM 47  H16 EMI 3  28.027  30.763   5.434  1.00  0.00
>> ATOM 48  H17 EMI 3  26.886  29.695   3.344  1.00  0.00
>> ATOM 49  H18 EMI 3  28.366  28.886   3.715  1.00  0.00
>> ATOM 50  H19 EMI 3  26.842  28.200   3.880  1.00  0.00
>> ATOM 51  S20 ETS 4  26.876  17.203   7.791  1.00  0.00
>> ATOM 52  O21 ETS 4  28.030  16.750   7.061  1.00  0.00
>> ATOM 53  O22 ETS 4  25.656  16.428   7.528  1.00  0.00
>> ATOM 54  O23 ETS 4  27.112  17.470   9.202  1.00  0.00
>> ATOM 55  O24 ETS 4  26.578  18.733   7.129  1.00  0.00
>> ATOM 56  C25 ETS 4  26.215  18.995   5.843  1.00  0.00
>> ATOM 57  C26 ETS 4  27.436  19.133   4.921  1.00  0.00
>> ATOM 58  H27 ETS 4  25.607  18.170   5.486  1.00  0.00
>> ATOM 59  H28 ETS 4  25.530  19.872   5.774  1.00  0.00
>> ATOM 60  H29 ETS 4  28.107  19.910   5.179  1.00  0.00
>> ATOM 61  H30 ETS 4  27.944  18.247   4.832  1.00  0.00
>> ATOM 62  H31 ETS 4  27.138  19.330   3.927  1.00  0.00
>> TER
>> ENDMDL
>
> 
>
>> [ molecules ]
>> ; Compound#mols
>> EMI 2
>> ETS 2
>>
>
> As I suspected, your molecules are simply out of order.  Your topology
> specifies
> EMI-EMI-ETS-ETS, but t

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Justin Lemkul




On 9/22/13 9:18 PM, Nilesh Dhumal wrote:

Sorry to paste big files here. (.pdb file and processed.top )


pdb file.

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00
ATOM 34  N3  EMI 3  25.074  30.288   7.940  1.00  0.00
ATOM 35  C4  EMI 3  26.335  30.336   7.464  1.00  0.00
ATOM 36  N5  EMI 3  26.369  29.867   6.216  1.00  0.00
ATOM 37  C6  EMI 3  27.586  29.761   5.460  1.00  0.00
ATOM 38  C7  EMI 3  27.397  29.088   4.106  1.00  0.00
ATOM 39  C8  EMI 3  24.601  30.404   9.351  1.00  0.00
ATOM 40  H9  EMI 3  24.815  29.446   4.790  1.00  0.00
ATOM 41  H10 EMI 3  23.203  29.817   6.920  1.00  0.00
ATOM 42  H11 EMI 3  27.238  30.558   8.074  1.00  0.00
ATOM 43  H12 EMI 3  24.321  29.435   9.759  1.00  0.00
ATOM 44  H13 EMI 3  25.411  30.876   9.880  1.00  0.00
ATOM 45  H14 EMI 3  23.735  31.092   9.515  1.00  0.00
ATOM 46  H15 EMI 3  28.216  29.130   6.169  1.00  0.00
ATOM 47  H16 EMI 3  28.027  30.763   5.434  1.00  0.00
ATOM 48  H17 EMI 3  26.886  29.695   3.344  1.00  0.00
ATOM 49  H18 EMI 3  28.366  28.886   3.715  1.00  0.00
ATOM 50  H19 EMI 3  26.842  28.200   3.880  1.00  0.00
ATOM 51  S20 ETS 4  26.876  17.203   7.791  1.00  0.00
ATOM 52  O21 ETS 4  28.030  16.750   7.061  1.00  0.00
ATOM 53  O22 ETS 4  25.656  16.428   7.528  1.00  0.00
ATOM 54  O23 ETS 4  27.112  17.470   9.202  1.00  0.00
ATOM 55  O24 ETS 4  26.578  18.733   7.129  1.00  0.00
ATOM 56  C25 ETS 4  26.215  18.995   5.843  1.00  0.00
ATOM 57  C26 ETS 4  27.436  19.133   4.921  1.00  0.00
ATOM 58  H27 ETS 4  25.607  18.170   5.486  1.00  0.00
ATOM 59  H28 ETS 4  25.530  19.872   5.774  1.00  0.00
ATOM 60  H29 ETS 4  28.107  19.910   5.179  1.00  0.00
ATOM 61  H30 ETS 4  27.944  18.247   4.832  1.00  0.00
ATOM 62  H31 ETS 4  27.138  19.330   3.927  1.00  0.00
TER
ENDMDL





[ molecules ]
; Compound#mols
EMI 2
ETS 2



As I suspected, your molecules are simply out of order.  Your topology specifies 
EMI-EMI-ETS-ETS, but the coordinate file lists the molecules as EMI-ETS-EMI-ETS, 
hence the mismatch.  The "Protein" [moleculetype] seems superfluous, but would 
be the appropriate solution for this case since it specifies EMI-ETS-EMI-ETS all 
in one [moleculetype] definition.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Nilesh Dhumal

Sorry to paste big files here. (.pdb file and processed.top )


pdb file.

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00
ATOM 34  N3  EMI 3  25.074  30.288   7.940  1.00  0.00
ATOM 35  C4  EMI 3  26.335  30.336   7.464  1.00  0.00
ATOM 36  N5  EMI 3  26.369  29.867   6.216  1.00  0.00
ATOM 37  C6  EMI 3  27.586  29.761   5.460  1.00  0.00
ATOM 38  C7  EMI 3  27.397  29.088   4.106  1.00  0.00
ATOM 39  C8  EMI 3  24.601  30.404   9.351  1.00  0.00
ATOM 40  H9  EMI 3  24.815  29.446   4.790  1.00  0.00
ATOM 41  H10 EMI 3  23.203  29.817   6.920  1.00  0.00
ATOM 42  H11 EMI 3  27.238  30.558   8.074  1.00  0.00
ATOM 43  H12 EMI 3  24.321  29.435   9.759  1.00  0.00
ATOM 44  H13 EMI 3  25.411  30.876   9.880  1.00  0.00
ATOM 45  H14 EMI 3  23.735  31.092   9.515  1.00  0.00
ATOM 46  H15 EMI 3  28.216  29.130   6.169  1.00  0.00
ATOM 47  H16 EMI 3  28.027  30.763   5.434  1.00  0.00
ATOM 48  H17 EMI 3  26.886  29.695   3.344  1.00  0.00
ATOM 49  H18 EMI 3  28.366  28.886   3.715  1.00  0.00
ATOM 50  H19 EMI 3  26.842  28.200   3.880  1.00  0.00
ATOM 51  S20 ETS 4  26.876  17.203   7.791  1.00  0.00
ATOM 52  O21 ETS 4  28.030  16.750   7.061  1.00  0.00
ATOM 53  O22 ETS 4  25.656  16.428   7.528  1.00  0.00
ATOM 54  O23 ETS 4  27.112  17.470   9.202  1.00  0.00
ATOM 55  O24 ETS 4  26.578  18.733   7.129  1.00  0.00
ATOM 56  C25 ETS 4  26.215  18.995   5.843  1.00  0.00
ATOM 57  C26 ETS 4  27.436  19.133   4.921  1.00  0.00
ATOM 58  H27 ETS 4  25.607  18.170   5.486  1.00  0.00
ATOM 59  H28 ETS 4  25.530  19.872   5.774  1.00  0.00
ATOM 60  H29 ETS 4  28.107  19.910   5.179  1.00  0.00
ATOM 61  H30 ETS 4  27.944  18.247   4.832  1.00  0.00
ATOM 62  H31 ETS 4  27.138  19.330   3.927  1.00  0.00
TER
ENDMDL


 processed.top
;
;   File 'p2.top' was generated
;   By user: ndhumal (36026)
;   On host: c63
;   At date: Sun Sep 22 21:03:07 2013
;
;   This is your topology file
;   Protein
;
; Include forcefield parameters

; This force field uses a format that requires Gromacs 3.1.4 or later.
;
; References for the OPLS-AA force field:
;
; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
; J. Am. Chem. Soc. 118, 11225-11236 (1996).
; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
; R. C. Rizzo and

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Justin Lemkul




On 9/22/13 8:54 PM, Nilesh Dhumal wrote:

Sorry to send email directly to your email address. Because of attachments
it not going through gmx_users.



The proper protocol is to post the files via publicly accessible URL so that 
anyone interested in helping may assist.



attached the topology file p2.top,
force field file glu-emi_lopes.itp and etso4.itp
molecule files emi.itp and ets.itp file.

I updated ffoplsaa.itp file as

#include "glu-emi_lop.itp"
#include "etso4.itp"
#include "emi.itp"
;#include "glu-emi_lop-modify.itp"
;#include "dmso-nilesh.itp"
;#include "ffoplsaanb.itp"
;#include "ffoplsaabon.itp"
;#include "pf6_opls.itp"
;#include "solvent.itp"
;#include "bmi1.itp"
;#include "acetate.itp"
;#include "pf6.itp"
#include "ets.itp"
;#include "water-flexiable.itp"



I'm not willing to hack my own force field files to make this work.  If you can 
provide a clean version, i.e. via a complete directory of modified files and/or 
post-processed topology from grompp -pp, that would be more useful and less 
error-prone.


Note that you did not send the coordinate file, which is critical information.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
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Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Justin Lemkul




On 9/22/13 7:13 PM, Nilesh Dhumal wrote:

Hello,

I am doing energy minimization for my system.  I am getting following
warnings

Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23)
Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24)
Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25)
Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26)
Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27)
Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28)
Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29)
Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30)
Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31)
Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C)
Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2)
Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3)
Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4)
Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5)
Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6)
Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7)
Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8)


Here is .pdb file

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00

and .top file is
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
chargeB  massB
  1   opls_561  1EMI  C  1  -0.13 12.011   ;
qtot -0.13
  2   opls_561  1EMI C2  2  -0.13 12.011   ;
qtot -0.26
  3   opls_557  1EMI N3  3   0.1514.0067   ;
qtot -0.11
  4   opls_558  1EMI C4  4  -0.11 12.011   ;
qtot -0.22
  5   opls_557  1EMI N5  5   0.1514.0067   ;
qtot -0.07
  6   opls_136  1EMI C6  6  -0.05 12.011   ;
qtot -0.12
  7   opls_135  1EMI C7  7  -0.17 12.011   ;
qtot -0.29
  8   opls_135  1EMI C8  8  -0.17 12.011   ;
qtot -0.46
  9   opls_564  1EMI H9  9   0.21  1.008   ;
qtot -0.25
 10   opls_564  1EMIH10  9   0.21  1.008   ;
qtot -0.04
 11   opls_563  1EMIH11  9   0.21  1.008   ;
qtot 0.17
 12   opls_140  1EMIH12 10   0.13  1.

[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

2013-09-22 Thread Nilesh Dhumal

Hello,

I am doing energy minimization for my system.  I am getting following
warnings

Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
Warning: atom name 23 in p2.top and p2.pdb does not match (C4 - O23)
Warning: atom name 24 in p2.top and p2.pdb does not match (N5 - O24)
Warning: atom name 25 in p2.top and p2.pdb does not match (C6 - C25)
Warning: atom name 26 in p2.top and p2.pdb does not match (C7 - C26)
Warning: atom name 27 in p2.top and p2.pdb does not match (C8 - H27)
Warning: atom name 28 in p2.top and p2.pdb does not match (H9 - H28)
Warning: atom name 29 in p2.top and p2.pdb does not match (H10 - H29)
Warning: atom name 30 in p2.top and p2.pdb does not match (H11 - H30)
Warning: atom name 31 in p2.top and p2.pdb does not match (H12 - H31)
Warning: atom name 32 in p2.top and p2.pdb does not match (H13 - C)
Warning: atom name 33 in p2.top and p2.pdb does not match (H14 - C2)
Warning: atom name 34 in p2.top and p2.pdb does not match (H15 - N3)
Warning: atom name 35 in p2.top and p2.pdb does not match (H16 - C4)
Warning: atom name 36 in p2.top and p2.pdb does not match (H17 - N5)
Warning: atom name 37 in p2.top and p2.pdb does not match (H18 - C6)
Warning: atom name 38 in p2.top and p2.pdb does not match (H19 - C7)
Warning: atom name 39 in p2.top and p2.pdb does not match (S20 - C8)


Here is .pdb file

TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1   34.775   34.775   34.775  90.00  90.00  90.00 P 1   1
MODEL1
ATOM  1  C   EMI 1   4.659  30.489  15.747  1.00  0.00
ATOM  2  C2  EMI 1   5.238  30.284  14.495  1.00  0.00
ATOM  3  N3  EMI 1   6.415  30.946  14.495  1.00  0.00
ATOM  4  C4  EMI 1   6.627  31.499  15.682  1.00  0.00
ATOM  5  N5  EMI 1   5.595  31.153  16.470  1.00  0.00
ATOM  6  C6  EMI 1   5.462  31.463  17.884  1.00  0.00
ATOM  7  C7  EMI 1   4.501  30.509  18.615  1.00  0.00
ATOM  8  C8  EMI 1   7.321  30.993  13.363  1.00  0.00
ATOM  9  H9  EMI 1   3.672  30.193  16.130  1.00  0.00
ATOM 10  H10 EMI 1   4.839  29.853  13.640  1.00  0.00
ATOM 11  H11 EMI 1   7.514  32.004  16.038  1.00  0.00
ATOM 12  H12 EMI 1   7.951  31.796  13.329  1.00  0.00
ATOM 13  H13 EMI 1   7.967  30.145  13.270  1.00  0.00
ATOM 14  H14 EMI 1   6.890  31.170  12.362  1.00  0.00
ATOM 15  H15 EMI 1   5.214  32.491  18.125  1.00  0.00
ATOM 16  H16 EMI 1   6.495  31.335  18.302  1.00  0.00
ATOM 17  H17 EMI 1   4.834  29.492  18.590  1.00  0.00
ATOM 18  H18 EMI 1   4.337  30.767  19.685  1.00  0.00
ATOM 19  H19 EMI 1   3.486  30.669  18.338  1.00  0.00
ATOM 20  S20 ETS 2  13.817   2.976  33.669  1.00  0.00
ATOM 21  O21 ETS 2  15.031   2.685  34.347  1.00  0.00
ATOM 22  O22 ETS 2  14.005   3.313  32.237  1.00  0.00
ATOM 23  O23 ETS 2  12.775   1.970  33.860  1.00  0.00
ATOM 24  O24 ETS 2  13.303   4.314  34.278  1.00  0.00
ATOM 25  C25 ETS 2  12.361   5.280  33.781  1.00  0.00
ATOM 26  C26 ETS 2  12.277   6.501  34.666  1.00  0.00
ATOM 27  H27 ETS 2  12.582   5.675  32.806  1.00  0.00
ATOM 28  H28 ETS 2  11.377   4.787  33.550  1.00  0.00
ATOM 29  H29 ETS 2  11.686   6.245  35.492  1.00  0.00
ATOM 30  H30 ETS 2  13.256   6.810  34.975  1.00  0.00
ATOM 31  H31 ETS 2  11.856   7.349  34.171  1.00  0.00
ATOM 32  C   EMI 3  25.075  29.706   5.816  1.00  0.00
ATOM 33  C2  EMI 3  24.256  29.876   6.894  1.00  0.00

and .top file is
[ atoms ]
;   nr   type  resnr residue  atom   cgnr charge   mass  typeB
   chargeB  massB
 1   opls_561  1EMI  C  1  -0.13 12.011   ;
qtot -0.13
 2   opls_561  1EMI C2  2  -0.13 12.011   ;
qtot -0.26
 3   opls_557  1EMI N3  3   0.1514.0067   ;
qtot -0.11
 4   opls_558  1EMI C4  4  -0.11 12.011   ;
qtot -0.22
 5   opls_557  1EMI N5  5   0.1514.0067   ;
qtot -0.07
 6   opls_136  1EMI C6  6  -0.05 12.011   ;
qtot -0.12
 7   opls_135  1EMI C7  7  -0.17 12.011   ;
qtot -0.29
 8   opls_135  1EMI C8  8  -0.17 12.011   ;
qtot -0.46
 9   opls_564  1EMI H9  9   0.21  1.008   ;
qtot -0.25
10   opls_564  1EMIH10  9   0.21  1.008   ;
qtot -0.04
11   opls_563  1EMIH11  9   0.21  1.008   ;
qtot 0.17
12   opls_140  1EMIH12 10   0.13  1.008   ;
qtot 0.3
13   opls_140  1EMIH13

Re: [gmx-users] restarting the crashed run

2013-09-22 Thread Mark Abraham

No, because then the state.cpt file would be redundant :-) All you can
do re-start from the beginning, because the .tpr file only has the
initial state. You can "extend" the number of steps, but you can't
magically produce the state after the first simulation just from the
initial one. (If you can, you'll be hugely popular here, though!)

Mark

On Sun, Sep 22, 2013 at 12:03 PM, Nidhi Katyal
 wrote:
> Thank you Justin for your reply.
> Pt 3 should be the correct way to proceed. But somehow if I have lost my
> state.cpt file, can I continue my run using following commands:
>
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene
> -noappend
> trjcat -f previous.trr next.trr -o combine.trr
>
>
>
>
> On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul  wrote:
>
>>
>>
>> On 9/21/13 3:46 PM, Nidhi Katyal wrote:
>>
>>> Dear all
>>> I would like to know the difference between restarting our crashed runs by
>>> 1) first generating next.tpr using tpbconv -extend option
>>>  then running grompp with this *.tpr file
>>>
>>
>> Why would you run grompp?  If you're using it as a source of coordinates,
>> you're going to be dealing with the initial state, not the last state of
>> the previous simulation, so that's garbage.  If you're restarting a crash,
>> then presumably there is no need at all to invoke tpbconv or grompp.
>>
>>
>>   and finally running mdrun but with no cpi option
>>>
>>
>> Makes no sense.  You're basically obliterating the previous simulation.
>>
>>
>>  2) same as 1 but with -cpi option
>>>
>>
>> Still no need for grompp, but if providing -cpi to mdrun, you're resuming
>> from the correct state.
>>
>>
>>  3) using only mdrun command with cpi option and with previous *.tpr
>>>  (ie not creating new tpr by tpbconv option)
>>>
>>
>> This is the correct way to proceed.  The run will pick up from the state
>> stored in the .cpt file and proceed with the number of steps originally
>> specified in the .tpr file.
>>
>>
>>  4) using procedure 3 but with no state.cpt file
>>>
>>>
>> The run should start over.
>>
>>
>>  Secondly, if state.cpt contains all the information to continue the
>>> simulation then why the simulation should continue at all without
>>> providing
>>> these files as in procedure 1 and 4
>>>
>>>
>> Without a .cpt file, the run starts over from the beginning.
>>
>> -Justin
>>
>> --
>> ==**
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul@outerbanks.umaryland.**edu  |
>> (410) 706-7441
>>
>> ==**
>> --
>> 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/Searchbefore
>>  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
>>
> --
> 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
-- 
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 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] restarting the crashed run

2013-09-22 Thread Nidhi Katyal

Thank you Justin for your reply.
Pt 3 should be the correct way to proceed. But somehow if I have lost my
state.cpt file, can I continue my run using following commands:

tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene
-noappend
trjcat -f previous.trr next.trr -o combine.trr




On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul  wrote:

>
>
> On 9/21/13 3:46 PM, Nidhi Katyal wrote:
>
>> Dear all
>> I would like to know the difference between restarting our crashed runs by
>> 1) first generating next.tpr using tpbconv -extend option
>>  then running grompp with this *.tpr file
>>
>
> Why would you run grompp?  If you're using it as a source of coordinates,
> you're going to be dealing with the initial state, not the last state of
> the previous simulation, so that's garbage.  If you're restarting a crash,
> then presumably there is no need at all to invoke tpbconv or grompp.
>
>
>   and finally running mdrun but with no cpi option
>>
>
> Makes no sense.  You're basically obliterating the previous simulation.
>
>
>  2) same as 1 but with -cpi option
>>
>
> Still no need for grompp, but if providing -cpi to mdrun, you're resuming
> from the correct state.
>
>
>  3) using only mdrun command with cpi option and with previous *.tpr
>>  (ie not creating new tpr by tpbconv option)
>>
>
> This is the correct way to proceed.  The run will pick up from the state
> stored in the .cpt file and proceed with the number of steps originally
> specified in the .tpr file.
>
>
>  4) using procedure 3 but with no state.cpt file
>>
>>
> The run should start over.
>
>
>  Secondly, if state.cpt contains all the information to continue the
>> simulation then why the simulation should continue at all without
>> providing
>> these files as in procedure 1 and 4
>>
>>
> Without a .cpt file, the run starts over from the beginning.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  |
> (410) 706-7441
>
> ==**
> --
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Re: [gmx-users] Re: No such moleculetype SOL

[gmx-users] Re: No such moleculetype SOL

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

[gmx-users] grompp Warning: atom name 20 in p2.top and p2.pdb does not match

Re: [gmx-users] restarting the crashed run

Re: [gmx-users] restarting the crashed run

11 matches

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