<div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hello Justin, sorry for the delay but I was trying repeat all my steps once more so that I was sure that the error would come out the same. It did.</blockquote>
<div>Here is a part of my itp file:<br>;<br>; File '1vkxdna_A.itp' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Wed Aug 27 11:46:27 2008<br>;<br>; This is your include topology file<br>
; MY_DUPLEX<br>;<br>[ moleculetype ]<br>; Name nrexcl<br>Protein_A 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br> 1 amber99_25 1 DT5 H5T 1 0.4422 1.008 ; qtot 0.4422<br>
2 amber99_43 1 DT5 O5' 2 -0.6318 16 ; qtot -0.1896<br> 3 amber99_11 1 DT5 C5' 3 -0.0069 12.01 ; qtot -0.1965<br> 4 amber99_19 1 DT5 H5'1 4 0.0754 1.008 ; qtot -0.1211<br>
5 amber99_19 1 DT5 H5'2 5 0.0754 1.008 ; qtot -0.0457<br> 6 amber99_11 1 DT5 C4' 6 0.1629 12.01 ; qtot 0.1172<br> 7 amber99_19 1 DT5 H4' 7 0.1176 1.008 ; qtot 0.2348<br>
8 amber99_44 1 DT5 O4' 8 -0.3691 16 ; qtot -0.1343<br> 9 amber99_11 1 DT5 C1' 9 0.068 12.01 ; qtot -0.0663<br> 10 amber99_20 1 DT5 H1' 10 0.1804 1.008 ; qtot 0.1141<br>
11 amber99_40 1 DT5 N1 11 -0.0239 14.01 ; qtot 0.0902<br> 12 amber99_7 1 DT5 C6 12 -0.2209 12.01 ; qtot -0.1307<br> 13 amber99_23 1 DT5 H6 13 0.2607 1.008 ; qtot 0.13<br>
14 amber99_7 1 DT5 C5 14 0.0025 12.01 ; qtot 0.1325<br> 15 amber99_11 1 DT5 C7 15 -0.2269 12.01 ; qtot -0.0944<br> 16 amber99_18 1 DT5 H71 16 0.077 1.008 ; qtot -0.0174<br>
17 amber99_18 1 DT5 H72 17 0.077 1.008 ; qtot 0.0596<br> 18 amber99_18 1 DT5 H73 18 0.077 1.008 ; qtot 0.1366<br> 19 amber99_2 1 DT5 C4 19 0.5194 12.01 ; qtot 0.656<br>
20 amber99_41 1 DT5 O4 20 -0.5563 16 ; qtot 0.0997<br> 21 amber99_35 1 DT5 N3 21 -0.434 14.01 ; qtot -0.3343<br> 22 amber99_25 1 DT5 H3 22 0.4422 1.008 ; qtot 0.1079<br>
23 amber99_2 1 DT5 C2 23 0.5677 12.01 ; qtot 0.6756<br> 24 amber99_41 1 DT5 O 24 -0.5881 16 ; qtot 0.0875<br> 25 amber99_11 1 DT5 C3' 25 0.0713 12.01 ; qtot 0.1588<br>
26 amber99_19 1 DT5 H3' 26 0.0985 1.008 ; qtot 0.2573<br> 27 amber99_11 1 DT5 C2' 27 -0.0854 12.01 ; qtot 0.1719<br> 28 amber99_18 1 DT5 H2'1 28 0.0718 1.008 ; qtot 0.2437<br>
29 amber99_18 1 DT5 H2'2 29 0.0718 1.008 ; qtot 0.3155<br> 30 amber99_44 1 DT5 O3' 30 -0.5232 16 ; qtot -0.2077<br><br>Here is my pdb2gmx command line:<br>
pdb2gmx -f 1vkxdna.pdb -p 1vkxdna.top -o 1vkxdna.gro<br><br>System charge still comes out as a non integer charge.<br>System has non-zero total charge: -2.151740e+01<br>Thank you again and sorry for the delay<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
<br>
<br>
Ragnarok sdf wrote:<br>
<br>
> Tahnk you Justein for the reply.<br>
> I read again chapter 5, this time I tried to be more thorough, but still<br>
> I don't really understand why my topology is coming out bad. My .itp<br>
> files do not look like the one from the manual abou UREA. What i mean<br>
> is, the angles and bonds parts of the file have only 3 columns. Although<br>
> I read the manual, I am still not sure about the real problem here.<br>
<br>
There is no problem with only having three or four columns, per se. Amber<br>
topologies will be shown as such. The bonded parameters will be read from the<br>
ffamber*bon.itp file. Have you identified the atoms involved in the problematic<br>
bond(s) and angle(s)?<br>
<br>
> You mentioned that each residue should end up with an integer charge.<br>
> Well, mine don't.<br>
> What exactly do you mean with "post one of your nucleotides here"? From<br>
> my pdb file or from my itp generated files? The entire double helix with<br>
> all nucleotides or really just one of them?<br>
<br>
Post a single nucleotide from the topology. Sorry if I wasn't clear. What<br>
would be interesting to see is what charges and atom types you've been assigning<br>
to each nucleotide.<br>
<br>
> Sorry for asking these details. But I just want to make sure I don't<br>
> waste your time with useless posts.<br>
<br>
Much appreciated :)<br>
<br>
-Justin<br>
<br>
> Thank you again<br>
> And thank you in advance<br>
> Fabrício<br>
><br>
><br>
> ------------------------------------------------------------------------<br>
><br>
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<br>
--<br>
========================================<br>
<br>
Justin A. Lemkul<br>
Graduate Research Assistant<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Sat, 23 Aug 2008 23:29:33 +0300<br>
From: "Shay Amram" <<a href="mailto:shayamra@post.tau.ac.il">shayamra@post.tau.ac.il</a>><br>
Subject: RE: [gmx-users] groups to write to trr<br>
To: <<a href="mailto:vvchaban@gmail.com">vvchaban@gmail.com</a>>, "'Discussion list for GROMACS users'"<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:20080823202940.593C5BEF6@doar.tau.ac.il">20080823202940.593C5BEF6@doar.tau.ac.il</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I think you should try using:<br>
<br>
trjconv -f file.trr -o file_with_groups_of_interest.trr -n index.ndx<br>
<br>
<br>
<br>
You should create the relevant index group (that includes all atoms of<br>
interest) before invoking the above command. You'll be prompted to choose a<br>
group so choose the group you created and trjconv will write an output trr<br>
that includes the group you picked alone.<br>
<br>
<br>
<br>
Hope that helps.<br>
<br>
-Shay<br>
<br>
<br>
<br>
<br>
<br>
-----Original Message-----<br>
From: <a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>]<br>
On Behalf Of Vitaly Chaban<br>
Sent: Friday, August 22, 2008 14:05 PM<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] groups to write to trr<br>
<br>
<br>
<br>
Hi,<br>
<br>
<br>
<br>
Is it possible to write only the specified groups to the TRR<br>
<br>
trajectory like using xtc-grps key for XTC?<br>
<br>
<br>
<br>
We calculate VACFs and so need velocities to be written but only the<br>
<br>
velocity of some groups are of interest, not of all the particles. The<br>
<br>
"full" TRRs take extremely huge space...<br>
<br>
<br>
<br>
<br>
<br>
Thanks.<br>
<br>
<br>
<br>
--<br>
<br>
Vitaly V. Chaban<br>
<br>
School of Chemistry<br>
<br>
National University of Kharkiv<br>
<br>
Svoboda sq., 4, Kharkiv 61077, Ukraine<br>
<br>
email: <a href="mailto:chaban@univer.kharkov.ua">chaban@univer.kharkov.ua</a><br>
<br>
skype: vvchaban<br>
<br>
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</blockquote></div><br></div>