<div>Message: 2<br>Date: Tue, 15 Aug 2006 13:05:07 -0300<br>From: "Elias santos" <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:silvasantosster@gmail.com">silvasantosster@gmail.com</a>
><br>Subject: [gmx-users] clusters [4Fe-4S]+2<br>To: <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID:<br> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:97baf6380608150905m45e96665mb1be5943457ca9a6@mail.gmail.com">
97baf6380608150905m45e96665mb1be5943457ca9a6@mail.gmail.com</a>><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi !!<br>I to construct to the block for residuo FS4 of the two clusters in the .rtp<br>
file of the force field ffgmx with all the linkings, angles etc., beyond the<br>on and not on parameters. When I run pdb2gmx, it does not give menssagem of<br>error, but the linkings between the cysteins (SG) and atoms of iron do not
<br>appear in the topology (.top) file. Although I have edited the 1jnr.pdb,<br>including the conections between atoms of iron and organics atoms of the<br>cisteinas.<br>What it can be?<br>They help me please!<br>-------------- next part --------------
<br>An HTML attachment was scrubbed...<br>URL: <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/pipermail/gmx-users/attachments/20060815/7c158cea/attachment-0001.html" target="_blank">
http://www.gromacs.org/pipermail/gmx-users/attachments/20060815/7c158cea/attachment-0001.html</a><br><br>------------------------------<br><br>Message: 3<br>Date: Tue, 15 Aug 2006 18:33:44 +0200<br>From: "Tsjerk Wassenaar" <
<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>Subject: Re: [gmx-users] clusters [4Fe-4S]+2<br>To: "Discussion list for GROMACS users" <
<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID:<br> <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:8ff898150608150933l103408e5k41bf57b0c8535817@mail.gmail.com">
8ff898150608150933l103408e5k41bf57b0c8535817@mail.gmail.com</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br>Hi Elias,<br><br>pdb2gmx does not read CONECT records in the pdb file. You have to add
<br>S(Cys) - Fe bonds in the specbond.dat file. The cause for not getting<br>any errors is that pdb2gmx sees cysteines, which it can handle, and<br>iron ions, which it can handle. But it doesn't think of connecting<br>them and doesn't know how to.
<br><br>Besides, don't use the ffgmx force fields (browse the archives for<br>reasons why not).<br><br>Cheers,<br><br>Tsjerk<br><br>On 8/15/06, Elias santos <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:silvasantosster@gmail.com">
silvasantosster@gmail.com</a>> wrote:<br>><br>> Hi !!<br>> I to construct to the block for residuo FS4 of the two clusters in the .rtp<br>> file of the force field ffgmx with all the linkings, angles etc., beyond the
<br>> on and not on parameters. When I run pdb2gmx, it does not give menssagem of<br>> error, but the linkings between the cysteins (SG) and atoms of iron do not<br>> appear in the topology (.top) file. Although I have edited the
1jnr.pdb,<br>> including the conections between atoms of iron and organics atoms of the<br>> cisteinas.<br>> What it can be?<br>> They help me please!<br>> _______________________________________________<br>
> gmx-users mailing list <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">
http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please don't post (un)subscribe requests to the list. Use the<br>> www interface or send it to <a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org">
gmx-users-request@gromacs.org</a>.<br>> Can't post? Read<br>> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php
</a><br>><br> </div>
<div>Hi!!</div>
<div>
<div style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px">Which the force field can be used in this situation? </div>
<div style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px">As I fill the fields of the archive specbond.dat for linkings between atoms of Fe of residue FS4 and SG of residuo of cysteins.?
</div>
<div style="PADDING-RIGHT: 10px; PADDING-LEFT: 10px; PADDING-BOTTOM: 10px; PADDING-TOP: 10px">Elias </div></div>