[gmx-users] pdb2gmx error_ resall.c, line: 321
udaya kiran
kiran.udaya at gmail.com
Mon Jan 24 14:29:53 CET 2011
Dear Mark Abraham,
Thanks a lot. It helped me a lot..!!
yours sincerely,
Uday.
On Mon, Jan 24, 2011 at 2:08 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
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> 1. Re: Gromos96 manual and user guid (Justin A. Lemkul)
> 2. Re: PRODRG server (Justin A. Lemkul)
> 3. pdb2gmx error_ resall.c, line: 321 (udaya kiran)
> 4. Re: pdb2gmx error_ resall.c, line: 321 (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 24 Jan 2011 07:27:51 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Gromos96 manual and user guid
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D3D7047.5060907 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> mohsen ramezanpour wrote:
> > Dear All
> > I need GROMOS96 manual and user guid for my work.
> > Can you send it for me?
>
> This information is (unfortunately) proprietary. You have to purchase the
> GROMOS software suite to obtain it.
>
> -Justin
>
> > Thanks in advance for your help.
> >
>
> --
> ========================================
>
> 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: Mon, 24 Jan 2011 07:31:40 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] PRODRG server
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Message-ID: <4D3D712C.6070005 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> mohsen ramezanpour wrote:
> > Dear Dr.justin
> > Actually by doing this we are using two different force fields in one
> > simulation.
> > I had done it before and the result was that I discussed before in
> > gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
> > Then,this approch seems to doesn't work about my system.
> >
> > Then I want to find charges and charge groups for gromos 43A1 and
> > replace them for my drug(to edit PRODRG file manually) and work totally
> > in gromos 43A1.
>
> Please keep your story consistent. In the last message, you said you
> wanted to
> work completely within 53A6, so I advised you on how to do that, now you
> say
> that you're trying to work completely within 43A1.
>
> > Unfortunately I can't obtain these parameter.
>
> You certainly do have these parameters. 43A1 is part of the Gromacs
> installation; in the .rtp file you'll find all of the functional groups
> that
> were derived in 43A1, as applied to amino acids and a few other groups.
>
> > Please let me have if you have it.
> > Can I use some Ab Initio software for determining partial charges of my
> > drug?
> > for example ABINIT or Gaussian!
> >
>
> My paper that you said you read has discussion and recommendations on this
> point. But be very clear: none of the QM methods we tested were able to
> reproduce the charges that are assigned to known functional groups since
> the
> Gromos parameterization methodology calls for "empirical refinement."
> Thus,
> manual modification and thorough validation are always necessary.
>
> -Justin
>
> > Thanks in advance
> >
> > On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <jalemkul at vt.edu
> > <mailto:jalemkul at vt.edu>> wrote:
> >
> >
> >
> > mohsen ramezanpour wrote:
> >
> > Ok
> > then,I can use PRODRG server to generate .top and .gro files
> > for drug.
> > since it's reported charges are not very accurate ,we can
> > replace all charges completely with them in 53A6(if was present).
> > But it means we are working in 53A6 force field.
> > then,we must generate .top and .gro files for our protein with
> > 53A6 too.
> > and work completely with 53A6.
> > Am i right?
> > thanks in advance
> >
> >
> > That sounds like a reasonable approach. Be sure to validate the
> > drug topology. In my experience, this procedure is pretty good, but
> > you always have to convince reviewers...
> >
> > -Justin
> >
> >
> > On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul
> > <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> > <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> >
> >
> >
> > mohsen ramezanpour wrote:
> >
> > Dear Justin
> >
> > I read your articles about PRODRG server,they were very
> > useful.
> > But I have a question:
> > are charges of functional groups and generally other atom
> > groups
> > the same in all force fields?
> > Because you have modified charges of your molecules by
> > Gromos96
> > 53A6 while prodrg server is generating topology files in
> > 43A1.
> > I want to know can I replace charges from gromos 53A6 or
> > other
> > forcefields?
> > thanks in advance
> >
> >
> > Charges are not the same between force fields. We did our
> study
> > with 43A1 since that is what PRODRG purports to produce. I
> would
> > say that our recommendations carry to other Gromos force
> > fields, as
> > well, but don't take charges from 43A1 and apply them to
> > 53A6. Be
> > consistent within the force field.
> >
> > The atom types produced by PRODRG are largely shared between
> 43A1
> > and 53A6, so if you *completely* replace all charges with
> > those from
> > 53A6, you should have a topology that is compatible with 53A6.
> >
> > -Justin
> >
> > -- ========================================
> >
> > Justin A. Lemkul
> > Ph.D. Candidate
> > ICTAS Doctoral Scholar
> > MILES-IGERT Trainee
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> > 231-9080
> >
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > -- gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> >
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 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 <http://vt.edu> | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list gmx-users at gromacs.org
> > <mailto:gmx-users at gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 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
>
> ========================================
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 24 Jan 2011 13:53:19 +0100
> From: udaya kiran <kiran.udaya at gmail.com>
> Subject: [gmx-users] pdb2gmx error_ resall.c, line: 321
> To: gmx-users at gromacs.org
> Message-ID:
> <AANLkTinS0kYkOfnREV4GQdomvQWd+h1=qKAtGq4PLECm at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear GROMACS users,
>
> I have received the following error when trying to convert a pdb file
> (containing N-methylated L- Leucine residue) to gro format. I am using
> ffG53a6 forcefield.
>
>
> Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
>
> Select the Force Field:
> 0: GROMOS96 43a1 force field
> 1: GROMOS96 43a2 force field (improved alkane dihedrals)
> 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> 6: [DEPRECATED] Gromacs force field (see manual)
> 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
> 8: Encad all-atom force field, using scaled-down vacuum charges
> 9: Encad all-atom force field, using full solvent charges
> 4
> Opening library file ffG53a6.rtp
> Opening library file aminoacids.dat
> Opening library file aminoacids.dat
> WARNING: masses will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file atommass.dat
> Entries in atommass.dat: 178
> WARNING: vdwradii will be determined based on residue and atom names,
> this can deviate from the real mass of the atom type
> Opening library file vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file elements.dat
> Entries in elements.dat: 218
> Reading 16L6_6S17_start.pdb...
> WARNING: all CONECT records are ignored
> Read '6S17 ', 39 atoms
> Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
> 26 out of 26 lines of xlateat.dat converted succesfully
> Analyzing pdb file
> There are 1 chains and 0 blocks of water and 6 residues with 39 atoms
>
> chain #res #atoms
> 1 ' ' 6 39
>
> All occupancies are one
> Opening library file ffG53a6.atp
> Atomtype 1
> Reading residue database... (ffG53a6)
> Opening library file ffG53a6.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing impropers on same bond as a proper
>
> *-------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: resall.c, line: 321
>
> Fatal error:
> in .rtp file at line:
>
>
> -------------------------------------------------------
> *
>
> Could you please let me know what could be the problem..?
>
> yours sincerely,
> Uday.
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> ------------------------------
>
> Message: 4
> Date: Tue, 25 Jan 2011 00:08:03 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] pdb2gmx error_ resall.c, line: 321
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D3D79B3.5040101 at anu.edu.au>
> Content-Type: text/plain; charset="iso-8859-1"
>
> On 24/01/2011 11:53 PM, udaya kiran wrote:
> > Dear GROMACS users,
> >
> > I have received the following error when trying to convert a pdb file
> > (containing N-methylated L- Leucine residue) to gro format. I am
> > using ffG53a6 forcefield.
> >
> >
> > Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
> >
> > Select the Force Field:
> > 0: GROMOS96 43a1 force field
> > 1: GROMOS96 43a2 force field (improved alkane dihedrals)
> > 2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
> > 3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
> > 4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> > 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
> > 6: [DEPRECATED] Gromacs force field (see manual)
> > 7: [DEPRECATED] Gromacs force field with hydrogens for NMR
> > 8: Encad all-atom force field, using scaled-down vacuum charges
> > 9: Encad all-atom force field, using full solvent charges
> > 4
> > Opening library file ffG53a6.rtp
> > Opening library file aminoacids.dat
> > Opening library file aminoacids.dat
> > WARNING: masses will be determined based on residue and atom names,
> > this can deviate from the real mass of the atom type
> > Opening library file atommass.dat
> > Entries in atommass.dat: 178
> > WARNING: vdwradii will be determined based on residue and atom names,
> > this can deviate from the real mass of the atom type
> > Opening library file vdwradii.dat
> > Entries in vdwradii.dat: 28
> > Opening library file dgsolv.dat
> > Entries in dgsolv.dat: 7
> > Opening library file electroneg.dat
> > Entries in electroneg.dat: 71
> > Opening library file elements.dat
> > Entries in elements.dat: 218
> > Reading 16L6_6S17_start.pdb...
> > WARNING: all CONECT records are ignored
> > Read '6S17 ', 39 atoms
> > Opening library file /usr/local/gromacs/share/gromacs/top/xlateat.dat
> > 26 out of 26 lines of xlateat.dat converted succesfully
> > Analyzing pdb file
> > There are 1 chains and 0 blocks of water and 6 residues with 39 atoms
> >
> > chain #res #atoms
> > 1 ' ' 6 39
> >
> > All occupancies are one
> > Opening library file ffG53a6.atp
> > Atomtype 1
> > Reading residue database... (ffG53a6)
> > Opening library file ffG53a6.rtp
> > Using default: not generating all possible dihedrals
> > Using default: excluding 3 bonded neighbors
> > Using default: generating 1,4 H--H interactions
> > Using default: removing impropers on same bond as a proper
> >
> > *-------------------------------------------------------
> > Program pdb2gmx, VERSION 4.0.5
> > Source code file: resall.c, line: 321
> >
> > Fatal error:
> > in .rtp file at line:
> >
> >
> > -------------------------------------------------------
> > *
> >
> > Could you please let me know what could be the problem..?
>
> You've broken the format of the .rtp file used in ffG53a6. Use the
> "diff" tool to compare the "before" and "after" versions. Be sure you
> are using unix-style line endings.
>
> Mark
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