<div>Dear, </div>
<div> </div>
<div>Your tutorial for windows are lacking of proper guidence. You should post the steps to use it to make it more user friendly.</div>
<div> </div>
<div>As I have tried from last two months but after installing it I really don't know to execute commands on windows. If you can guide me then why don't you not tell me the steps for using it on windows. <br><br>
</div>
<div><span class="gmail_quote">On 11/10/09, <b class="gmail_sendername"><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a></b> <<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>> wrote:</span>
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<br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of gmx-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Missing H from residue (Jack Shultz)<br> 2. Re: Missing H from residue (Justin A. Lemkul)<br>
3. Re: Missing H from residue (Jack Shultz)<br> 4. Please tell me how to simulate two structures together in a<br> water box (radhika jaswal)<br> 5. (no subject) (pawan raghav)<br> 6. Re: (no subject) (Mark Abraham)<br>
<br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Mon, 9 Nov 2009 21:38:23 -0500<br>From: Jack Shultz <<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>><br>
Subject: Re: [gmx-users] Missing H from residue<br>To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br> <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Cc: Andrey Voronkov <<a href="mailto:av@drugdiscoveryathome.com">av@drugdiscoveryathome.com</a>><br>Message-ID:<br> <<a href="mailto:6c65435e0911091838x89cddeera26061500376e186@mail.gmail.com">6c65435e0911091838x89cddeera26061500376e186@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br><br>On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>><br>><br>> Jack Shultz wrote:<br>><br>
> <snip><br>><br>>> -------------------------------------------------------<br>>> Program pdb2gmx, VERSION 4.0.5<br>>> Source code file: pdb2gmx.c, line: 429<br>>><br>>> Fatal error:<br>
>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms<br>>> while sorting atoms<br>>> -------------------------------------------------------<br>>><br>>> But we got an O here<br>
>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00<br>>> O<br>>><br>><br>> The error is not telling you that the O atom is missing from the .pdb file;<br>> it is telling you that it is present in the .pdb, but not in the .rtp entry.<br>
> Look at the .rtp entry for CARG<br><br>[ CARG ]<br>[ atoms ]<br> N amber99_34 -0.34810 1<br> H amber99_17 0.27640 2<br> CA amber99_11 -0.30680 3<br> HA amber99_19 0.14470 4<br>
CB amber99_11 -0.03740 5<br> HB1 amber99_18 0.03710 6<br> HB2 amber99_18 0.03710 7<br> CG amber99_11 0.07440 8<br> HG1 amber99_18 0.01850 9<br> HG2 amber99_18 0.01850 10<br>
CD amber99_11 0.11140 11<br> HD1 amber99_19 0.04680 12<br> HD2 amber99_19 0.04680 13<br> NE amber99_38 -0.55640 14<br> HE amber99_17 0.34790 15<br> CZ amber99_3 0.83680 16<br>
NH1 amber99_38 -0.87370 17<br>HH11 amber99_17 0.44930 18<br>HH12 amber99_17 0.44930 19<br> NH2 amber99_38 -0.87370 20<br>HH21 amber99_17 0.44930 21<br>HH22 amber99_17 0.44930 22<br>
C amber99_2 0.85570 23<br> OC1 amber99_45 -0.82660 24<br> OC2 amber99_45 -0.82660 25<br><br>- you should have an O1 and O2 atom for the<br><br>I made the following modification<br>ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O<br>
ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O<br><br><br>-------------------------------------------------------<br>Program pdb2gmx, VERSION 4.0.5<br>Source code file: pdb2gmx.c, line: 429<br>
<br>Fatal error:<br>Atom O in residue CARG 122 not found in rtp entry with 25 atoms<br> while sorting atoms<br>-------------------------------------------------------<br><br><br>> C-terminal carboxylate.<br>
><br>> -Justin<br>><br>> --<br>> ========================================<br>><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>
> Blacksburg, VA<br>> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>> ========================================<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br><br>--<br>Jack<br><br><a href="http://drugdiscoveryathome.com">http://drugdiscoveryathome.com</a><br>
<a href="http://hydrogenathome.org">http://hydrogenathome.org</a><br><br><br>------------------------------<br><br>Message: 2<br>Date: Mon, 09 Nov 2009 22:00:05 -0500<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
Subject: Re: [gmx-users] Missing H from residue<br>To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4AF8D735.1030707@vt.edu">4AF8D735.1030707@vt.edu</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br><br><br>Jack Shultz wrote:<br>> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>
>><br>>> Jack Shultz wrote:<br>>><br>>> <snip><br>>><br>>>> -------------------------------------------------------<br>>>> Program pdb2gmx, VERSION 4.0.5<br>>>> Source code file: pdb2gmx.c, line: 429<br>
>>><br>>>> Fatal error:<br>>>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms<br>>>> while sorting atoms<br>>>> -------------------------------------------------------<br>
>>><br>>>> But we got an O here<br>>>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00<br>>>> O<br>>>><br>>> The error is not telling you that the O atom is missing from the .pdb file;<br>
>> it is telling you that it is present in the .pdb, but not in the .rtp entry.<br>>> Look at the .rtp entry for CARG<br>><br>> [ CARG ]<br>> [ atoms ]<br>> N amber99_34 -0.34810 1<br>
> H amber99_17 0.27640 2<br>> CA amber99_11 -0.30680 3<br>> HA amber99_19 0.14470 4<br>> CB amber99_11 -0.03740 5<br>> HB1 amber99_18 0.03710 6<br>
> HB2 amber99_18 0.03710 7<br>> CG amber99_11 0.07440 8<br>> HG1 amber99_18 0.01850 9<br>> HG2 amber99_18 0.01850 10<br>> CD amber99_11 0.11140 11<br>
> HD1 amber99_19 0.04680 12<br>> HD2 amber99_19 0.04680 13<br>> NE amber99_38 -0.55640 14<br>> HE amber99_17 0.34790 15<br>> CZ amber99_3 0.83680 16<br>
> NH1 amber99_38 -0.87370 17<br>> HH11 amber99_17 0.44930 18<br>> HH12 amber99_17 0.44930 19<br>> NH2 amber99_38 -0.87370 20<br>> HH21 amber99_17 0.44930 21<br>
> HH22 amber99_17 0.44930 22<br>> C amber99_2 0.85570 23<br>> OC1 amber99_45 -0.82660 24<br>> OC2 amber99_45 -0.82660 25<br>><br>> - you should have an O1 and O2 atom for the<br>
><br>> I made the following modification<br>> ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00 O<br>> ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00 O<br>
><br><br>Forgive my typo, what I meant was OC1 and OC2. You must always make sure the<br>atoms in the structure file match those expected by the .rtp file. You need OC1<br>and OC2.<br><br>-Justin<br><br>><br>> -------------------------------------------------------<br>
> Program pdb2gmx, VERSION 4.0.5<br>> Source code file: pdb2gmx.c, line: 429<br>><br>> Fatal error:<br>> Atom O in residue CARG 122 not found in rtp entry with 25 atoms<br>> while sorting atoms<br>
> -------------------------------------------------------<br>><br>><br>>> C-terminal carboxylate.<br>>><br>>> -Justin<br>>><br>>> --<br>>> ========================================<br>
>><br>>> Justin A. Lemkul<br>>> Ph.D. Candidate<br>>> ICTAS Doctoral Scholar<br>>> Department of Biochemistry<br>>> Virginia Tech<br>>> Blacksburg, VA<br>>> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>>><br>>> ========================================<br>>> --<br>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>>> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the www interface<br>>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
>><br>><br>><br>><br><br>--<br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>
<br><br>------------------------------<br><br>Message: 3<br>Date: Mon, 9 Nov 2009 22:10:22 -0500<br>From: Jack Shultz <<a href="mailto:js@drugdiscoveryathome.com">js@drugdiscoveryathome.com</a>><br>Subject: Re: [gmx-users] Missing H from residue<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br> <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a href="mailto:6c65435e0911091910r7c932c23l2a2814b72d8be69a@mail.gmail.com">6c65435e0911091910r7c932c23l2a2814b72d8be69a@mail.gmail.com</a>><br>
Content-Type: text/plain; charset=ISO-8859-1<br><br>Thanks Justin! Got it now.<br><br>On Mon, Nov 9, 2009 at 10:00 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>><br>><br>
> Jack Shultz wrote:<br>>><br>>> On Mon, Nov 9, 2009 at 8:35 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:<br>>>><br>>>> Jack Shultz wrote:<br>>>><br>
>>> <snip><br>>>><br>>>>> -------------------------------------------------------<br>>>>> Program pdb2gmx, VERSION 4.0.5<br>>>>> Source code file: pdb2gmx.c, line: 429<br>
>>>><br>>>>> Fatal error:<br>>>>> Atom O in residue CARG 244 not found in rtp entry with 25 atoms<br>>>>> while sorting atoms<br>>>>> -------------------------------------------------------<br>
>>>><br>>>>> But we got an O here<br>>>>> ATOM 3822 O CARG 153 -4.455 -21.080 2.791 1.00 0.00<br>>>>> O<br>>>>><br>>>> The error is not telling you that the O atom is missing from the .pdb<br>
>>> file;<br>>>> it is telling you that it is present in the .pdb, but not in the .rtp<br>>>> entry.<br>>>> Look at the .rtp entry for CARG<br>>><br>>> [ CARG ]<br>>> [ atoms ]<br>
>> N amber99_34 -0.34810 1<br>>> H amber99_17 0.27640 2<br>>> CA amber99_11 -0.30680 3<br>>> HA amber99_19 0.14470 4<br>>> CB amber99_11 -0.03740 5<br>
>> HB1 amber99_18 0.03710 6<br>>> HB2 amber99_18 0.03710 7<br>>> CG amber99_11 0.07440 8<br>>> HG1 amber99_18 0.01850 9<br>>> HG2 amber99_18 0.01850 10<br>
>> CD amber99_11 0.11140 11<br>>> HD1 amber99_19 0.04680 12<br>>> HD2 amber99_19 0.04680 13<br>>> NE amber99_38 -0.55640 14<br>>> HE amber99_17 0.34790 15<br>
>> CZ amber99_3 0.83680 16<br>>> NH1 amber99_38 -0.87370 17<br>>> HH11 amber99_17 0.44930 18<br>>> HH12 amber99_17 0.44930 19<br>>> NH2 amber99_38 -0.87370 20<br>
>> HH21 amber99_17 0.44930 21<br>>> HH22 amber99_17 0.44930 22<br>>> C amber99_2 0.85570 23<br>>> OC1 amber99_45 -0.82660 24<br>>> OC2 amber99_45 -0.82660 25<br>
>><br>>> - you should have an O1 and O2 atom for the<br>>><br>>> I made the following modification<br>>> ATOM 1900 O1 CARG 153 -17.391 -20.267 11.508 1.00 0.00<br>>> O<br>
>> ATOM 1909 O2 CARG 153 -18.666 -19.390 13.107 1.00 0.00<br>>> O<br>>><br>><br>> Forgive my typo, what I meant was OC1 and OC2. You must always make sure<br>> the atoms in the structure file match those expected by the .rtp file. You<br>
> need OC1 and OC2.<br>><br>> -Justin<br>><br>>><br>>> -------------------------------------------------------<br>>> Program pdb2gmx, VERSION 4.0.5<br>>> Source code file: pdb2gmx.c, line: 429<br>
>><br>>> Fatal error:<br>>> Atom O in residue CARG 122 not found in rtp entry with 25 atoms<br>>> while sorting atoms<br>>> -------------------------------------------------------<br>
>><br>>><br>>>> C-terminal carboxylate.<br>>>><br>>>> -Justin<br>>>><br>>>> --<br>>>> ========================================<br>>>><br>>>> Justin A. Lemkul<br>
>>> Ph.D. Candidate<br>>>> ICTAS Doctoral Scholar<br>>>> Department of Biochemistry<br>>>> Virginia Tech<br>>>> Blacksburg, VA<br>>>> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>
>>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>>>><br>>>> ========================================<br>>>> --<br>
>>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>>>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>>> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before<br>>>> posting!<br>>>> Please don't post (un)subscribe requests to the list. Use the www<br>
>>> interface<br>>>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>>>> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>
>>><br>>><br>>><br>>><br>><br>> --<br>> ========================================<br>><br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>
> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]<a href="http://vt.edu">vt.edu</a> | (540) 231-9080<br>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>> ========================================<br>> --<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface<br>> or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br><br>--<br>Jack<br><br><a href="http://drugdiscoveryathome.com">http://drugdiscoveryathome.com</a><br>
<a href="http://hydrogenathome.org">http://hydrogenathome.org</a><br><br><br>------------------------------<br><br>Message: 4<br>Date: Tue, 10 Nov 2009 12:10:57 +0530 (IST)<br>From: radhika jaswal <<a href="mailto:jaswalradhika@yahoo.co.in">jaswalradhika@yahoo.co.in</a>><br>
Subject: [gmx-users] Please tell me how to simulate two structures<br> together in a water box<br>To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: <<a href="mailto:864176.49303.qm@web94808.mail.in2.yahoo.com">864176.49303.qm@web94808.mail.in2.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br><br>Respected Sir,<br><br>Please tell me how to simulate two different stuctures together in a<br>water box so as to have an idea of drug docking and what options to<br>
use. Any suggestions are welcome.<br><br><br><br>With Regards<br><br>Radhika<br><br><br><br><br><br><br> Connect more, do more and share more with Yahoo! India Mail. Learn more. <a href="http://in.overview.mail.yahoo.com/">http://in.overview.mail.yahoo.com/</a><br>
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<br>------------------------------<br><br>Message: 5<br>Date: Tue, 10 Nov 2009 12:16:56 +0530<br>From: pawan raghav <<a href="mailto:pwnrghv@gmail.com">pwnrghv@gmail.com</a>><br>Subject: [gmx-users] (no subject)<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a href="mailto:c7ae933b0911092246he5f982fyad982886dfe5cb6c@mail.gmail.com">c7ae933b0911092246he5f982fyad982886dfe5cb6c@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br><br>After installing gromacs4.0 on windows it created Gromacs directory<br>containing several .exe files in bin directory. But when I used pdb2gmx<br>command it will shows that basch command is not found. So anyone can tell me<br>
what is that.<br><br>--<br>Pawan Kumar Raghav<br>Bioinformatician<br>Stem Cell and Gene Therapy Research Group<br>INMAS, DRDO<br>Timarpur Delhi-110054<br>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>
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<br>Message: 6<br>Date: Tue, 10 Nov 2009 17:59:19 +1100<br>From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>Subject: Re: [gmx-users] (no subject)<br>To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4AF90F47.8030805@anu.edu.au">4AF90F47.8030805@anu.edu.au</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>pawan raghav wrote:<br>> After installing gromacs4.0 on windows it created Gromacs directory<br>
> containing several .exe files in bin directory. But when I used pdb2gmx<br>> command it will shows that basch command is not found. So anyone can<br>> tell me what is that.<br><br>See point 8 here<br><a href="http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions">http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions</a><br>
<br>Mark<br><br><br>------------------------------<br><br>--<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br><br>End of gmx-users Digest, Vol 67, Issue 60<br>*****************************************<br></blockquote>
</div><br><br clear="all"><br>-- <br>Pawan Kumar Raghav<br>Bioinformatician<br>Stem Cell and Gene Therapy Research Group<br>INMAS, DRDO<br>Timarpur Delhi-110054