[gmx-users] Number of cooredinate in topol.top and solv.gro not matching
Sangita Kachhap
sangita at imtech.res.in
Wed May 2 19:09:49 CEST 2012
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> Today's Topics:
>
> 1. Re: How to remove H atom from residue in gro file?
> (Justin A. Lemkul)
> 2. Re: How to remove H atom from residue in gro file? (Mark Abraham)
> 3. Re: Number of coordinate in topol.top and solv.gro not
> matching (Justin A. Lemkul)
> 4. Re: Automation of selecting water around a molecule (Mark Abraham)
> 5. ???? ????? (Shima Arasteh)
> 6. Re: GROMOS87 and CHARMM27 (Justin A. Lemkul)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 02 May 2012 09:09:39 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] How to remove H atom from residue in gro
> file?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA13213.2040305 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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>
>
> On 5/2/12 6:55 AM, Hagit G wrote:
>> Hi gmx users,
>>
>>
>> Well, I saw this question but the answer was not understood.
>> I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a
>> disulfide bond. Gromacs automatically adds H atoms.
>> Although the disulfide bond is there, Gromacs ignore it because *each cystein
>> is
>> on a different chain*. So it adds H and therefor the disulfide bond is ruined
>> during energy minimization.
>> Is there any way to recreate such a disulfide bond (Please don't tell me again
>> about "-ss" it works only on one chain. Moreover, the bond is existed on the
>> pdf
>> file.) or never ruined it at the first place?
>>
>
> Well you may need to use -ss, but since you don't want to hear about it, I won't
> say anything more...
>
> What you need to do is create a [moleculetype] that consists of both chains.
> The pdb2gmx option -chainsep will allow you to create a properly merged molecule
> that can form the intermolecular disulfide because the two molecules will be
> considered as one [moleculetype], as Gromacs requires.
>
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 02 May 2012 23:11:08 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] How to remove H atom from residue in gro
> file?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA1326C.6080905 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 2/05/2012 8:55 PM, Hagit G wrote:
>> Hi gmx users,
>>
>> Well, I saw this question but the answer was not understood.
>> I'm trying to work with the file 1PPB.pdb. There are 2 chains
>> connected with a disulfide bond. Gromacs automatically adds H atoms.
>> Although the disulfide bond is there, Gromacs ignore it because *each
>> cystein is on a different chain*. So it adds H and therefor the
>> disulfide bond is ruined during energy minimization.
>> Is there any way to recreate such a disulfide bond (Please don't tell
>> me again about "-ss" it works only on one chain. Moreover, the bond is
>> existed on the pdf file.) or never ruined it at the first place?
>
> Yes, and the clue to how to combine the chains to give the mechanism a
> chance of working is on the page I linked last time:
> http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds
>
> Mark
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> ------------------------------
>
> Message: 3
> Date: Wed, 02 May 2012 09:12:13 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Number of coordinate in topol.top and
> solv.gro not matching
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA132AD.1060202 at vt.edu>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
>
> On 5/2/12 8:14 AM, Sangita Kachhap wrote:
>>
>> Hello all
>>
>> I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
>> Thus I am doing tutorialfor Protein - Ligand tutorial:
>>
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
>>
>> I have used following command:
>>
>> pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
>>
>> editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
>>
>> genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
>>
>> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>>
>> I am getting stuck at last command. Its showing following error:
>>
>> Fatal error:
>> number of coordinates in coordinate file (solv.gro, 33049)
>> does not match topology (topol.top, 33064)
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>
> Did you follow the link? Did you read
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
> ?
>
>> {But when I calculate number of atom in topol.top and solv.gro it is same}
>>
>
> That's not possible.
>
>> When I checked above http: I got that such type of error may be due to cpp
>> variable is not properly set in the .mdp file.
>> But When I locate ccp in my system and add it to .mdp file.
>>
>> "
>> ; LINES STARTING WITH ';' ARE COMMENTS
>> title = Minimization ; Title of run
>> cpp =/usr/bin/cpp
>> ; Parameters describing what to do, when to stop and what to save
>> "
>>
>> Then also it showing same error.
>>
>> Please help me to solve this problem.
>>
>> I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
>>
>
> The cpp parameter is ignored for all Gromacs versions as of 4.5.
>
> Your problem is that you don't have a ligand in your coordinate file. Note that
> you're off by 15 atoms, which is exactly how many are in the ligand described in
> the tutorial. Go back and read the instructions closely, as appending the
> ligand to the protein coordinate file is discussed in detail.
Thanks for reply
When I am appending ligand from .gro file and generating complex the new .gro
file newbox.gro do not have ligand.
Command I have used: editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
I am appending ligand like this at the end of conf.gro
163ASN HD21 1689 1.029 -0.671 -0.401
163ASN HD22 1690 0.944 -0.584 -0.525
163ASN C 1691 0.621 -0.740 -0.126
163ASN O1 1692 0.624 -0.616 -0.140
163ASN O2 1693 0.683 -0.703 -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C14 2 2.392 -2.470 -0.139
1JZ4 C13 3 2.246 -2.441 -0.181
1JZ4 C12 4 2.229 -2.519 -0.308
1JZ4 C11 5 2.169 -2.646 -0.295
1JZ4 H11 6 2.135 -2.683 -0.199
1JZ4 C7 7 2.155 -2.721 -0.411
1JZ4 H7 8 2.104 -2.817 -0.407
1JZ4 C8 9 2.207 -2.675 -0.533
1JZ4 H8 10 2.199 -2.738 -0.621
1JZ4 C9 11 2.267 -2.551 -0.545
1JZ4 H9 12 2.306 -2.516 -0.640
1JZ4 C10 13 2.277 -2.473 -0.430
1JZ4 OAB 14 2.341 -2.354 -0.434
1JZ4 HAB 15 2.369 -2.334 -0.528
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000 0.00000
0.00000
I am also adding following to topol.top.
; Include ligand topology
#include "drg.itp"
&
JZ4 1
> -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
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 02 May 2012 23:18:28 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Automation of selecting water around a
> molecule
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA13424.3060605 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 2/05/2012 7:49 PM, Lara Bunte wrote:
>> Hi
>>
>> I need a little help in using Linux. I wrote this script for the bash, that I
>> called g_select_script.sh:
>>
>>
>> #!/bin/bash
>> g_select -s mol_in_water.pdb -select '"Close to ISO" resname SOL and within
>> 0.4 of resname ISO' -on
>> make_ndx -f mol_in_water.pdb -o index2.ndx
>> cat index2.ndx index.ndx> index3.ndx
>> make_ndx -f mol_in_water.pdb -n index3.ndx -o index_final.ndx
>> trjconv -n index_final.ndx -f mol_in_water.pdb -s mol_in_water.pdb -o
>> output.pdb
>>
>>
>> After this I make a file called parameters_for_g_select_script, that looks
>> like:
>>
>> 2
>> q
>> 2|7
>> q
>> 8
>>
>> And finally I type in the bash this command:
>>
>>
>> ./g_select_script.sh< parameters_for_g_select_script
>>
>> Sadly this does not work. It works correct until make_ndx -f mol_in_water.pdb
>> -n index3.ndx -o index_final.ndx with parameters 2|7 and q
>>
>> The numbers of the groups are correct. I guess, that 2|7 is not transfered
>> correctly. I tried '2|7' and "2|7" that also do not work.
>>
>>
>> What is wrong in my automation? Please help a Linux noob like me.
>
> Not sure, but maybe the shell redirection of the file to stdin
> interprets the pipe symbol as it would on the command line. If so,
> "escaping" it as 2\|7 may work. Or as Teemu suggests, g_select is a more
> expressive tool once you wrap your brain around it. You should be able
> to get away with a 2-line script needing no redirection in most (all?)
> cases.
>
> A further clue - groups can be identified by name in GROMACS, so you can
> make your scripting more meaningful and resilient to change by referring
> to groups by name rather than number. Next month, you'll have no idea
> what 2, 7 and 8 are, but their names you'll still understand, hopefully!
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 2 May 2012 07:33:39 -0700 (PDT)
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> Subject: [gmx-users] ???? ?????
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <1335969219.7601.YahooMailNeo at web36407.mail.mud.yahoo.com>
> Content-Type: text/plain; charset="utf-8"
>
>
>
> ????????
> ???? ?????????? ????????. ???? ?????? ?????? ???????? ???????????? ?????? ??????
> ????????????. ???????? ?????? ?????????????? ???????? ?????????? ?????? ??????
> ????????????
> ????????
> ???????? ??????????
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> Message: 6
> Date: Wed, 02 May 2012 10:32:59 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] GROMOS87 and CHARMM27
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4FA1459B.1000602 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 5/2/12 10:30 AM, Shima Arasteh wrote:
>>
>> Thanks for your reply.
>>
>> What do you mean by running for some additional time?
>
> You're introducing a new force field, which includes different representation of
> atoms and a different potential energy function. You can't just take a
> configuration generated by Gromos87, apply CHARMM27 parameters to it, and expect
> continuity in the job. You need to re-equilibrate the structure under the new
> parameters.
>
>> I guess,I have to modulate the structure from the first point. Right? I think
>> the results of last run using gromos is not beneficial at all, because the
>> parameters are different for sure.
>>
>
> Having little idea what you're doing, I'll tend to agree.
>
> -Justin
>
>> Cheers,
>> Shima
>>
>> --------------------------------------------------------------------------------
>> *From:* Justin A. Lemkul <jalemkul at vt.edu>
>> *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS
>> users <gmx-users at gromacs.org>
>> *Sent:* Wednesday, May 2, 2012 5:34 PM
>> *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
>>
>>
>>
>> On 5/2/12 12:21 AM, Shima Arasteh wrote:
>> >
>> > Dear Justin,
>> > I don't want to compare the forcefields results.
>> > Yes, Iwant to use some old information in conjunction with something new.
>> > In fact, I have to regenerate a structure, which has modulated using
>> gmx.ff.
>> > After it, I am going to study it using umbrella sampling technique. I want
>> to do
>> > it using charmm27. I want to know if it is possible? Is it correct that I
>> use
>> > the results of the job done by gmx? Or I need to repeat the job using
>> charmm?
>> >
>>
>> Structures are force field agnostic. You can process them with whatever force
>> field you like. If the structure you want to simulate with CHARMM was previous
>> produced by Gromos87 (as I suspect, from looking at the thread below) then you
>> will definitely need to run for some additional time. The force field is
>> different and thus you need to re-equilibrate the system (at the very least)
>> under the new parameters.
>>
>> -Justin
>>
>> > Thanks,
>> > Shima
>> >
>> > --------------------------------------------------------------------------------
>> > *From:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>> > *To:* Shima Arasteh <shima_arasteh2001 at yahoo.com
>> <mailto:shima_arasteh2001 at yahoo.com>>; Discussion list for GROMACS
>> > users <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>> > *Sent:* Tuesday, May 1, 2012 9:44 PM
>> > *Subject:* Re: Fw: [gmx-users] GROMOS87 and CHARMM27
>> >
>> >
>> >
>> > On 5/1/12 1:08 PM, Shima Arasteh wrote:
>> > >
>> > >
>> > > One more question:
>> > > But what about of using the potential surface?
>> > > In fact, I want to use the results of modeling in umbrella sampling. Is
>> it
>> > possible?
>> > >
>> >
>> > I, for one, am not clear what you are asking. Are you trying to compare
>> force
>> > field results? Build a system based off another? Use some old information
>> in
>> > conjunction with something new (i.e. force field mixing, which is a bad
>> idea)?
>> >
>> > -Justin
>> >
>> > > Thanks in advance,
>> > > Shima
>> > >
>> > >
>> --------------------------------------------------------------------------------
>> > > *From:* Peter C. Lai <pcl at uab.edu <mailto:pcl at uab.edu>
>> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>>>
>> > > *To:* Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>
>> > > *Sent:* Monday, April 16, 2012 9:50 PM
>> > > *Subject:* Re: [gmx-users] GROMOS87 and CHARMM27
>> > >
>> > > On 2012-04-16 10:14:01AM -0700, Shima Arasteh wrote:
>> > > > So, I can not use the coordinates of the output files of gromos runs.
>> Right?
>> > >
>> > > You can but you may need to rename the atoms for each residue for pdb2gmx
>> > > to work.
>> > >
>> > > >
>> > > >
>> > > > ________________________________
>> > > > From: Peter C. Lai <pcl at uab.edu <mailto:pcl at uab.edu>
>> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>
>> > <mailto:pcl at uab.edu <mailto:pcl at uab.edu>>>>
>> > > > To: Discussion list for GROMACS users <gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>> > > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>>>
>> > > > Sent: Monday, April 16, 2012 8:23 PM
>> > > > Subject: Re: [gmx-users] GROMOS87 and CHARMM27
>> > > >
>> > > > On 2012-04-16 08:26:00AM -0700, Shima Arasteh wrote:
>> > > > > Dear GROMACS users,
>> > > > >
>> > > > > I reproduced the results of a protein-membrane system by using force
>> field
>> > > GROMOSE87. This protein forms ion channel in membrane.
>> > > > > Now if I wanna study the ion conduction through this channel using
>> force
>> > > field CHARMM27 in umbrella sampling method, is it possible? Can I use the
>> > > results of the system simulation which has been derived by GROMOS87?
>> > > >
>> > > > By definition, switching to a different forcefield like that usually
>> requires
>> > > > the regeneration of the system's topology, so your new system will be
>> > > > different from your old one anyway. In addition, you may need to rename
>> the
>> > > > atoms in the coordinate files obtained from previous gromos runs to
>> match
>> > > > those in the charmm27 residue files.
>> > > >
>> > > > --
>> > > > ==================================================================
>> > > > Peter C. Lai | University of Alabama-Birmingham
>> > > > Programmer/Analyst | KAUL 752A
>> > > > Genetics, Div. of Research | 705 South 20th Street
>> > > > pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>
>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu>>>
>> > | Birmingham AL 35294-4461
>> > > > (205) 690-0808 |
>> > > > ==================================================================
>> > > >
>> > > > --
>> > > > gmx-users mailing list gmx-users at gromacs.org
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>> > > > Please search the archive at
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>> > >
>> > > --
>> > > ==================================================================
>> > > Peter C. Lai | University of Alabama-Birmingham
>> > > Programmer/Analyst | KAUL 752A
>> > > Genetics, Div. of Research | 705 South 20th Street
>> > > pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>>
>> <mailto:pcl at uab.edu <mailto:pcl at uab.edu> <mailto:pcl at uab.edu
>> <mailto:pcl at uab.edu>>> |
>> > Birmingham AL 35294-4461
>> > > (205) 690-0808 |
>> > > ==================================================================
>> > >
>> > > --
>> > > gmx-users mailing list gmx-users at gromacs.org
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>> > > Please search the archive at
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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
>> >
>> > ========================================
>> >
>> >
>> >
>> >
>> >
>> >
>>
>> --
>> ========================================
>>
>> 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
>>
>> ========================================
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> --
> gmx-users mailing list
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> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> before posting!
>
> End of gmx-users Digest, Vol 97, Issue 15
> *****************************************
>
With regards
Sangita Kachhap
SRF
BIC,IMTECH
CHANDIGARH
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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