[gmx-users] Simulation of Primed DNA-rtp entry and Terminal residue

Singh raghavbioinfo at gmail.com
Wed Jul 6 15:25:47 CEST 2011


Hi  Justin,

Thanks for quick response :)

Basically I don't want terminal H atom.. instead of that I want O+ at 3' end and -CH2-O-PO3 at second. but it is appearing on both the ends... :( 

Any suggestions?

Raghav 
Research Scholar
IEMN, University of Science and Technology
Villeneuve d'ascq, Lille, France




On 6 juil. 2011, at 15:08, gmx-users-request at gromacs.org wrote:

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>   1. Re: Register (Rossen Apostolov)
>   2. Re: make a new bond in VERSION 4.5.4 (Justin A. Lemkul)
>   3. Re: Questions about GB parameters (Justin A. Lemkul)
>   4. Re: Simulation of Primed DNA (Singh)
>   5. Re: Simulation of Primed DNA (Justin A. Lemkul)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Wed, 06 Jul 2011 13:35:40 +0300
> From: Rossen Apostolov <rossen at kth.se>
> Subject: Re: [gmx-users] Register
> To: Saeid Akbarshahi <saeidakbarshahi at yahoo.com>, 	Discussion list for
> 	GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E143A7C.20408 at kth.se>
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> You can only register from the website:
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> Rossen
> 
> 
> ------------------------------
> 
> Message: 2
> Date: Wed, 06 Jul 2011 07:00:11 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] make a new bond in VERSION 4.5.4
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E14403B.1020902 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Yulian Gavrilov wrote:
>> Dear Justin, gmx users,
>> 
>> I forgot to write, but I added these new residues to aminoacids.rtp.
>> 
>> Maybe I need to add them also to aminoacids.r2b? How to do it correctly? 
> 
> An .r2b entry is unnecessary in this case; these files are only used to 
> standardize force field-specific names for certain residues.
> 
>> Just new lines in it or add them to lines of Gly and Lys? So, I suppose 
>> it is all steps in 
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>> 
> 
> These should be all the necessary steps.
> 
> -Justin
> 
>> 
>> [ LYQ ]
>> 
>> [ atoms ]
>> 
>> N N -0.41570 1
>> 
>> H H 0.27190 2
>> 
>> CA CT -0.07206 3
>> 
>> HA H1 0.09940 4
>> 
>> CB CT -0.04845 5
>> 
>> HB1 HC 0.03400 6
>> 
>> HB2 HC 0.03400 7
>> 
>> CG CT 0.06612 8
>> 
>> HG1 HC 0.01041 9
>> 
>> HG2 HC 0.01041 10
>> 
>> CD CT -0.03768 11
>> 
>> HD1 HC 0.01155 12
>> 
>> HD2 HC 0.01155 13
>> 
>> CE CT 0.32604 14
>> 
>> HE1 HP -0.03358 15
>> 
>> HE2 HP -0.03358 16
>> 
>> NZ N -0.64977 17
>> 
>> HZ1 H 0.38604 18
>> 
>> C C 0.59730 19
>> 
>> O O -0.56790 20
>> 
>> [ bonds ]
>> 
>> N H
>> 
>> N CA
>> 
>> CA HA
>> 
>> CA CB
>> 
>> CA C
>> 
>> CB HB1
>> 
>> CB HB2
>> 
>> CB CG
>> 
>> CG HG1
>> 
>> CG HG2
>> 
>> CG CD
>> 
>> CD HD1
>> 
>> CD HD2
>> 
>> CD CE
>> 
>> CE HE1
>> 
>> CE HE2
>> 
>> CE NZ
>> 
>> NZ HZ1
>> 
>> C O
>> 
>> -C N
>> 
>> [ impropers ]
>> 
>> -C CA N H
>> 
>> CA +N C O
>> 
>> 
>> 
>> [ GLQ ]
>> 
>> [ atoms ]
>> 
>> N N -0.41570 1
>> 
>> H H 0.27190 2
>> 
>> CA CT -0.02520 3
>> 
>> HA1 H1 0.06980 4
>> 
>> HA2 H1 0.06980 5
>> 
>> C C 0.59730 6
>> 
>> O O -0.56790 7
>> 
>> [ bonds ]
>> 
>> N H
>> 
>> N CA
>> 
>> CA HA1
>> 
>> CA HA2
>> 
>> CA C
>> 
>> C O
>> 
>> -C N
>> 
>> [ impropers ]
>> 
>> -C CA N H
>> 
>> CA +N C O
>> 
>> 
>> -- 
>> 
>> Sincerely,
>> 
>> Yulian Gavrilov
>> 
>> 
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 06 Jul 2011 08:02:09 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Questions about GB parameters
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E144EC1.1060008 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Per Larsson wrote:
>> Hi!
>> 
>> Yes, I did! Had to look up a conversation between me and the Tinker
>> developers about precisely this.
>> 
>> The values are indeed not the original ones, but rather developed internally
>> by Tinker people so to minimise differences between analytical surface areas
>> and GB, given the HCT-algorithm and using per-atom rather than per-pair scale
>> factors. The values have not been published anywhere as such but "have been
>> used by others and seem fairly robust", according to Tinker developers.
>> 
>> In the light of all other approximations introduced with implicit solvent,
>> the differences in results should be minor.
>> 
>> Of course this needs to be properly documented, and it was very good that
>> some light was shed on this.
>> 
> 
> Great, thanks for clarifying all of this!  I will make a note to adjust the 
> documentation.  At the moment, it sounds as if one should expect the exact HCT 
> pairwise scaling method, which is obviously not the case.
> 
> -Justin
> 
>> /Per
>> 
>> 
>> 6 jul 2011 kl. 04:29 skrev "Justin A. Lemkul" <jalemkul at vt.edu>:
>> 
>>> 
>>> Per Larsson wrote:
>>>> Hi! I did some digging and think I can clarify at least the first
>>>> question. Sorry for the confusion with regard to the earlier post. What
>>>> is specified in the gbsa.itp file under the gbr column is indeed
>>>> vdW-radii. These are used to compute Born radii, as the manual says. The
>>>> dielectric offset is subtracted from the vdW radii, as this has been
>>>> shown to improve the agreement between PB and GB calculations (see eg.
>>>> the OBC-paper, Onufriev, Bashford and Case, Proteins, 55, 383-394). For
>>>> the second question, I am a little confused myself now. The values found 
>>>> in the gbsa.itp-file are exactly those found in the Tinker package (in
>>>> the ksolv.f-routine), which also cites the same reference. Hmm...I'll be
>>>> back again for this one.
>>> Have you uncovered anything?  I've tried contacting the Tinker developers
>>> but have received no response.  I found the routine (in Tinker's born.f)
>>> that utilizes the values, but I still have no idea where they come from or
>>> why they're fixed for a given atom type rather than a given pair.
>>> 
>>> -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
>>> 
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>> 
>> 
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================
> 
> 
> ------------------------------
> 
> Message: 4
> Date: Wed, 6 Jul 2011 14:52:47 +0200
> From: Singh <raghavbioinfo at gmail.com>
> Subject: Re: [gmx-users] Simulation of Primed DNA
> To: gmx-users at gromacs.org
> Message-ID: <04C1557F-4654-4C30-9509-2011D5CF8294 at gmail.com>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi all, 
> 
> As per Justin's suggestion , I have created a rtp entry for primed THY  residue..which is like this ..
> 
> [ DT5P ]
> [ atoms ]
>   H5T    HO            0.44220     1
>   O5'    O            -0.63180     2
>   C5'    CT           -0.00690     3
>  H5'1    H1            0.07540     4
>  H5'2    H1            0.07540     5
>   C4'    CT            0.16290     6
>   H4'    H1            0.11760     7
>   O4'    OS           -0.36910     8
>   C1'    CT            0.06800     9
>   H1'    H2            0.18040    10
>    N1    N*           -0.02390    11
>    C6    CM           -0.22090    12
>    H6    H4            0.26070    13
>    C5    CM            0.00250    14
>    C7    CT           -0.22690    15
>   H71    HC            0.07700    16
>   H72    HC            0.07700    17
>   H73    HC            0.07700    18
>    C4    C             0.51940    19
>    O4    O            -0.55630    20
>    N3    NA           -0.43400    21
>    H3    H             0.34200    22
>    C2    C             0.56770    23
>    O2    O            -0.58810    24
>   C3'    CT            0.07130    25
>   H3'    H1            0.09850    26
>   C2'    CT           -0.08540    27
>  H2'1    HC            0.07180    28
>  H2'2    HC            0.07180    29
>   O3'    OS           -0.52320    30
>   P      P             1.16590    31
>   O1P    O2           -0.77610    32
>   O2P    O2           -0.77610    33
>   O3P	  O2           -0.77610    34                
> [ bonds ]
>   O5'   P
>   O5'   C5'
>   C5'  H5'1
>   C5'  H5'2
>   C5'   C4'
>   C4'   H4'
>   C4'   O4'
>   C4'   C3'
>   O4'   C1'
>   C1'   H1'
>   C1'    N1
>   C1'   C2'
>    N1    C6
>    N1    C2
>    C6    H6
>    C6    C5
>    C5    C7
>    C5    C4
>    C7   H71
>    C7   H72
>    C7   H73
>    C4    O4
>    C4    N3
>    N3    H3
>    N3    C2
>    C2    O2
>   C3'   H3'
>   C3'   C2'
>   C3'   O3'
>   C2'  H2'1
>   C2'  H2'2
> [ impropers ]
>    C2    C6    N1   C1'
>    C4    C6    C5    C7
>    N1    N3    C2    O2
>    C5    N3    C4    O4
>    C4    C2    N3    H3  
>    N1    C5    C6    H6
> 
> and the THY with terminal Phosphate group is...
> 
> ATOM      1  O5'  DT A   1      -5.444  -3.882 -27.274  1.00  0.00           O  
> ATOM      2  C5'  DT A   1      -4.975  -5.193 -26.943  1.00  0.00           C  
> ATOM      3 1H5'  DT A   1      -4.594  -5.667 -27.848  1.00  0.00           H  
> ATOM      4 2H5'  DT A   1      -5.809  -5.781 -26.560  1.00  0.00           H  
> ATOM      5  C4'  DT A   1      -3.861  -5.152 -25.898  1.00  0.00           C  
> ATOM      6  H4'  DT A   1      -3.531  -6.170 -25.685  1.00  0.00           H  
> ATOM      7  O4'  DT A   1      -2.738  -4.387 -26.383  1.00  0.00           O  
> ATOM      8  C1'  DT A   1      -2.272  -3.512 -25.342  1.00  0.00           C  
> ATOM      9  H1'  DT A   1      -1.204  -3.694 -25.215  1.00  0.00           H  
> ATOM     10  N1   DT A   1      -2.478  -2.073 -25.683  1.00  0.00           N  
> ATOM     11  C6   DT A   1      -3.733  -1.556 -25.872  1.00  0.00           C  
> ATOM     12  H6   DT A   1      -4.556  -2.210 -26.150  1.00  0.00           H  
> ATOM     13  C2   DT A   1      -1.358  -1.256 -25.798  1.00  0.00           C  
> ATOM     14  O2   DT A   1      -0.205  -1.685 -25.775  1.00  0.00           O  
> ATOM     15  N3   DT A   1      -1.613   0.096 -25.966  1.00  0.00           N  
> ATOM     16  H3   DT A   1      -0.819   0.705 -26.089  1.00  0.00           H  
> ATOM     17  C4   DT A   1      -2.857   0.699 -25.989  1.00  0.00           C  
> ATOM     18  O4   DT A   1      -2.954   1.918 -26.111  1.00  0.00           O  
> ATOM     19  C5   DT A   1      -3.955  -0.231 -25.855  1.00  0.00           C  
> ATOM     20  C7   DT A   1      -5.368   0.283 -25.580  1.00  0.00           C  
> ATOM     21  H71  DT A   1      -5.381   1.373 -25.594  1.00  0.00           H  
> ATOM     22  H72  DT A   1      -5.685  -0.067 -24.597  1.00  0.00           H  
> ATOM     23  H73  DT A   1      -6.051  -0.098 -26.340  1.00  0.00           H  
> ATOM     24  C2'  DT A   1      -2.985  -4.008 -24.085  1.00  0.00           C  
> ATOM     25 2H2'  DT A   1      -2.460  -4.883 -23.698  1.00  0.00           H  
> ATOM     26 1H2'  DT A   1      -3.043  -3.243 -23.310  1.00  0.00           H  
> ATOM     27  C3'  DT A   1      -4.324  -4.508 -24.586  1.00  0.00           C  
> ATOM     28  H3'  DT A   1      -4.981  -3.657 -24.744  1.00  0.00           H  
> ATOM     29  O3'  DT A   1      -4.947  -5.483 -23.741  1.00  0.00           O  
> ATOM     30  P    DT A   1      -6.751  -3.677 -28.479  1.00  0.00           P  
> ATOM     31  O1P  DT A   1      -7.056  -2.218 -28.645  1.00  0.00           O  
> ATOM     32  O2P  DT A   1      -7.982  -4.394 -28.010  1.00  0.00           O1-
> ATOM     33  O3P  DT A   1      -6.283  -4.285 -29.883  1.00  0.00           O 
> 
> 
> ...it started creating top and Gro files but.. when I checked visually by VMD i found that in Gro file an H is placed between CH2O and PHOSPHATE group while in my pdb it's a proper terminal... like  , -CH2O-PO3..?
> 
> Can anyone suggest me any further changes I am supposed to made in these files !
> 
> Raghav
> 
> 
> 
> ------------------------------
> 
> Message: 5
> Date: Wed, 06 Jul 2011 09:07:47 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Simulation of Primed DNA
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E145E23.70307 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 
> 
> Singh wrote:
>> Hi all, 
>> 
>> As per Justin's suggestion , I have created a rtp entry for primed THY  residue..which is like this ..
>> 
>> [ DT5P ]
>> [ atoms ]
>>   H5T    HO            0.44220     1
>>   O5'    O            -0.63180     2
>>   C5'    CT           -0.00690     3
>>  H5'1    H1            0.07540     4
>>  H5'2    H1            0.07540     5
>>   C4'    CT            0.16290     6
>>   H4'    H1            0.11760     7
>>   O4'    OS           -0.36910     8
>>   C1'    CT            0.06800     9
>>   H1'    H2            0.18040    10
>>    N1    N*           -0.02390    11
>>    C6    CM           -0.22090    12
>>    H6    H4            0.26070    13
>>    C5    CM            0.00250    14
>>    C7    CT           -0.22690    15
>>   H71    HC            0.07700    16
>>   H72    HC            0.07700    17
>>   H73    HC            0.07700    18
>>    C4    C             0.51940    19
>>    O4    O            -0.55630    20
>>    N3    NA           -0.43400    21
>>    H3    H             0.34200    22
>>    C2    C             0.56770    23
>>    O2    O            -0.58810    24
>>   C3'    CT            0.07130    25
>>   H3'    H1            0.09850    26
>>   C2'    CT           -0.08540    27
>>  H2'1    HC            0.07180    28
>>  H2'2    HC            0.07180    29
>>   O3'    OS           -0.52320    30
>>   P      P             1.16590    31
>>   O1P    O2           -0.77610    32
>>   O2P    O2           -0.77610    33
>>   O3P	  O2           -0.77610    34                
>> [ bonds ]
>>   O5'   P
>>   O5'   C5'
>>   C5'  H5'1
>>   C5'  H5'2
>>   C5'   C4'
>>   C4'   H4'
>>   C4'   O4'
>>   C4'   C3'
>>   O4'   C1'
>>   C1'   H1'
>>   C1'    N1
>>   C1'   C2'
>>    N1    C6
>>    N1    C2
>>    C6    H6
>>    C6    C5
>>    C5    C7
>>    C5    C4
>>    C7   H71
>>    C7   H72
>>    C7   H73
>>    C4    O4
>>    C4    N3
>>    N3    H3
>>    N3    C2
>>    C2    O2
>>   C3'   H3'
>>   C3'   C2'
>>   C3'   O3'
>>   C2'  H2'1
>>   C2'  H2'2
>> [ impropers ]
>>    C2    C6    N1   C1'
>>    C4    C6    C5    C7
>>    N1    N3    C2    O2
>>    C5    N3    C4    O4
>>    C4    C2    N3    H3  
>>    N1    C5    C6    H6
>> 
>> and the THY with terminal Phosphate group is...
>> 
>> ATOM      1  O5'  DT A   1      -5.444  -3.882 -27.274  1.00  0.00           O  
>> ATOM      2  C5'  DT A   1      -4.975  -5.193 -26.943  1.00  0.00           C  
>> ATOM      3 1H5'  DT A   1      -4.594  -5.667 -27.848  1.00  0.00           H  
>> ATOM      4 2H5'  DT A   1      -5.809  -5.781 -26.560  1.00  0.00           H  
>> ATOM      5  C4'  DT A   1      -3.861  -5.152 -25.898  1.00  0.00           C  
>> ATOM      6  H4'  DT A   1      -3.531  -6.170 -25.685  1.00  0.00           H  
>> ATOM      7  O4'  DT A   1      -2.738  -4.387 -26.383  1.00  0.00           O  
>> ATOM      8  C1'  DT A   1      -2.272  -3.512 -25.342  1.00  0.00           C  
>> ATOM      9  H1'  DT A   1      -1.204  -3.694 -25.215  1.00  0.00           H  
>> ATOM     10  N1   DT A   1      -2.478  -2.073 -25.683  1.00  0.00           N  
>> ATOM     11  C6   DT A   1      -3.733  -1.556 -25.872  1.00  0.00           C  
>> ATOM     12  H6   DT A   1      -4.556  -2.210 -26.150  1.00  0.00           H  
>> ATOM     13  C2   DT A   1      -1.358  -1.256 -25.798  1.00  0.00           C  
>> ATOM     14  O2   DT A   1      -0.205  -1.685 -25.775  1.00  0.00           O  
>> ATOM     15  N3   DT A   1      -1.613   0.096 -25.966  1.00  0.00           N  
>> ATOM     16  H3   DT A   1      -0.819   0.705 -26.089  1.00  0.00           H  
>> ATOM     17  C4   DT A   1      -2.857   0.699 -25.989  1.00  0.00           C  
>> ATOM     18  O4   DT A   1      -2.954   1.918 -26.111  1.00  0.00           O  
>> ATOM     19  C5   DT A   1      -3.955  -0.231 -25.855  1.00  0.00           C  
>> ATOM     20  C7   DT A   1      -5.368   0.283 -25.580  1.00  0.00           C  
>> ATOM     21  H71  DT A   1      -5.381   1.373 -25.594  1.00  0.00           H  
>> ATOM     22  H72  DT A   1      -5.685  -0.067 -24.597  1.00  0.00           H  
>> ATOM     23  H73  DT A   1      -6.051  -0.098 -26.340  1.00  0.00           H  
>> ATOM     24  C2'  DT A   1      -2.985  -4.008 -24.085  1.00  0.00           C  
>> ATOM     25 2H2'  DT A   1      -2.460  -4.883 -23.698  1.00  0.00           H  
>> ATOM     26 1H2'  DT A   1      -3.043  -3.243 -23.310  1.00  0.00           H  
>> ATOM     27  C3'  DT A   1      -4.324  -4.508 -24.586  1.00  0.00           C  
>> ATOM     28  H3'  DT A   1      -4.981  -3.657 -24.744  1.00  0.00           H  
>> ATOM     29  O3'  DT A   1      -4.947  -5.483 -23.741  1.00  0.00           O  
>> ATOM     30  P    DT A   1      -6.751  -3.677 -28.479  1.00  0.00           P  
>> ATOM     31  O1P  DT A   1      -7.056  -2.218 -28.645  1.00  0.00           O  
>> ATOM     32  O2P  DT A   1      -7.982  -4.394 -28.010  1.00  0.00           O1-
>> ATOM     33  O3P  DT A   1      -6.283  -4.285 -29.883  1.00  0.00           O 
>> 
>> 
>> ...it started creating top and Gro files but.. when I checked visually by VMD i found that in Gro file an H is placed between CH2O and PHOSPHATE group while in my pdb it's a proper terminal... like  , -CH2O-PO3..?
>> 
>> Can anyone suggest me any further changes I am supposed to made in these files !
>> 
> 
> I don't see how this worked in the first place.  You've defined a residue named 
> "DT5P" but then expect that to be mapped onto "DT" (which it should not).  Are 
> you reconstructing H positions via an .hdb entry as well?  I suspect you have to 
> be, due to the absence of H5T, which is in the .rtp entry but not the .pdb 
> coordinates.  If an H atom is being placed strangely, then probably you've not 
> assigned the correct geometry in the .hdb entry.  See the manual.
> 
> -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
> 
> ========================================
> 
> 
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> End of gmx-users Digest, Vol 87, Issue 32
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