[gmx-users] Re: gmx-users Digest, Vol 52, Issue 97
Ragnarok sdf
fabracht1 at gmail.com
Wed Aug 27 16:59:46 CEST 2008
>
> 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.
Here is a part of my itp file:
;
; File '1vkxdna_A.itp' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Wed Aug 27 11:46:27 2008
;
; This is your include topology file
; MY_DUPLEX
;
[ moleculetype ]
; Name nrexcl
Protein_A 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
1 amber99_25 1 DT5 H5T 1 0.4422 1.008 ; qtot
0.4422
2 amber99_43 1 DT5 O5' 2 -0.6318 16 ; qtot
-0.1896
3 amber99_11 1 DT5 C5' 3 -0.0069 12.01 ; qtot
-0.1965
4 amber99_19 1 DT5 H5'1 4 0.0754 1.008 ; qtot
-0.1211
5 amber99_19 1 DT5 H5'2 5 0.0754 1.008 ; qtot
-0.0457
6 amber99_11 1 DT5 C4' 6 0.1629 12.01 ; qtot
0.1172
7 amber99_19 1 DT5 H4' 7 0.1176 1.008 ; qtot
0.2348
8 amber99_44 1 DT5 O4' 8 -0.3691 16 ; qtot
-0.1343
9 amber99_11 1 DT5 C1' 9 0.068 12.01 ; qtot
-0.0663
10 amber99_20 1 DT5 H1' 10 0.1804 1.008 ; qtot
0.1141
11 amber99_40 1 DT5 N1 11 -0.0239 14.01 ; qtot
0.0902
12 amber99_7 1 DT5 C6 12 -0.2209 12.01 ; qtot
-0.1307
13 amber99_23 1 DT5 H6 13 0.2607 1.008 ; qtot
0.13
14 amber99_7 1 DT5 C5 14 0.0025 12.01 ; qtot
0.1325
15 amber99_11 1 DT5 C7 15 -0.2269 12.01 ; qtot
-0.0944
16 amber99_18 1 DT5 H71 16 0.077 1.008 ; qtot
-0.0174
17 amber99_18 1 DT5 H72 17 0.077 1.008 ; qtot
0.0596
18 amber99_18 1 DT5 H73 18 0.077 1.008 ; qtot
0.1366
19 amber99_2 1 DT5 C4 19 0.5194 12.01 ; qtot
0.656
20 amber99_41 1 DT5 O4 20 -0.5563 16 ; qtot
0.0997
21 amber99_35 1 DT5 N3 21 -0.434 14.01 ; qtot
-0.3343
22 amber99_25 1 DT5 H3 22 0.4422 1.008 ; qtot
0.1079
23 amber99_2 1 DT5 C2 23 0.5677 12.01 ; qtot
0.6756
24 amber99_41 1 DT5 O 24 -0.5881 16 ; qtot
0.0875
25 amber99_11 1 DT5 C3' 25 0.0713 12.01 ; qtot
0.1588
26 amber99_19 1 DT5 H3' 26 0.0985 1.008 ; qtot
0.2573
27 amber99_11 1 DT5 C2' 27 -0.0854 12.01 ; qtot
0.1719
28 amber99_18 1 DT5 H2'1 28 0.0718 1.008 ; qtot
0.2437
29 amber99_18 1 DT5 H2'2 29 0.0718 1.008 ; qtot
0.3155
30 amber99_44 1 DT5 O3' 30 -0.5232 16 ; qtot
-0.2077
Here is my pdb2gmx command line:
pdb2gmx -f 1vkxdna.pdb -p 1vkxdna.top -o 1vkxdna.gro
System charge still comes out as a non integer charge.
System has non-zero total charge: -2.151740e+01
Thank you again and sorry for the delay
>
>
>
> Ragnarok sdf wrote:
>
> > Tahnk you Justein for the reply.
> > I read again chapter 5, this time I tried to be more thorough, but still
> > I don't really understand why my topology is coming out bad. My .itp
> > files do not look like the one from the manual abou UREA. What i mean
> > is, the angles and bonds parts of the file have only 3 columns. Although
> > I read the manual, I am still not sure about the real problem here.
>
> There is no problem with only having three or four columns, per se. Amber
> topologies will be shown as such. The bonded parameters will be read from
> the
> ffamber*bon.itp file. Have you identified the atoms involved in the
> problematic
> bond(s) and angle(s)?
>
> > You mentioned that each residue should end up with an integer charge.
> > Well, mine don't.
> > What exactly do you mean with "post one of your nucleotides here"? From
> > my pdb file or from my itp generated files? The entire double helix with
> > all nucleotides or really just one of them?
>
> Post a single nucleotide from the topology. Sorry if I wasn't clear. What
> would be interesting to see is what charges and atom types you've been
> assigning
> to each nucleotide.
>
> > Sorry for asking these details. But I just want to make sure I don't
> > waste your time with useless posts.
>
> Much appreciated :)
>
> -Justin
>
> > Thank you again
> > And thank you in advance
> > Fabrício
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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: Sat, 23 Aug 2008 23:29:33 +0300
> From: "Shay Amram" <shayamra at post.tau.ac.il>
> Subject: RE: [gmx-users] groups to write to trr
> To: <vvchaban at gmail.com>, "'Discussion list for GROMACS users'"
> <gmx-users at gromacs.org>
> Message-ID: <20080823202940.593C5BEF6 at doar.tau.ac.il>
> Content-Type: text/plain; charset="us-ascii"
>
> I think you should try using:
>
> trjconv -f file.trr -o file_with_groups_of_interest.trr -n index.ndx
>
>
>
> You should create the relevant index group (that includes all atoms of
> interest) before invoking the above command. You'll be prompted to choose
> a
> group so choose the group you created and trjconv will write an output trr
> that includes the group you picked alone.
>
>
>
> Hope that helps.
>
> -Shay
>
>
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Vitaly Chaban
> Sent: Friday, August 22, 2008 14:05 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] groups to write to trr
>
>
>
> Hi,
>
>
>
> Is it possible to write only the specified groups to the TRR
>
> trajectory like using xtc-grps key for XTC?
>
>
>
> We calculate VACFs and so need velocities to be written but only the
>
> velocity of some groups are of interest, not of all the particles. The
>
> "full" TRRs take extremely huge space...
>
>
>
>
>
> Thanks.
>
>
>
> --
>
> Vitaly V. Chaban
>
> School of Chemistry
>
> National University of Kharkiv
>
> Svoboda sq., 4, Kharkiv 61077, Ukraine
>
> email: chaban at univer.kharkov.ua
>
> skype: vvchaban
>
> _______________________________________________
>
> gmx-users mailing list gmx-users at gromacs.org
>
> http://www.gromacs.org/mailman/listinfo/gmx-users
>
> Please search the archive at http://www.gromacs.org/search before posting!
>
> Please don't post (un)subscribe requests to the list. Use the
>
> www interface or send it to gmx-users-request at gromacs.org.
>
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://www.gromacs.org/pipermail/gmx-users/attachments/20080823/448e53db/attachment.html
>
> ------------------------------
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
>
> End of gmx-users Digest, Vol 52, Issue 97
> *****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20080827/27d1c6a7/attachment.html>
More information about the gromacs.org_gmx-users
mailing list