[gmx-users] want to remove H5T entry form HDB file / open terminal (P, O) for polymerization of i-motif
raghav singh
raghavbioinfo at gmail.com
Fri Jul 8 15:06:16 CEST 2011
Hi Justin, All,
This is my recent log of PDB2GMX command... I have got what I wanted but I
would really appreciate if one you experts have a look and let me know
weather everything is fine.
I have not calculated new charge distribution after removing the entries for
H5T and H3T .. so here I have found non integral charges on molecule..
(which I am going to do right now).
Thanks Justin for your valuable suggestions.. :)
Thankfully
Raghav
Select the Force Field:
>From current directory:
1: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
>From '/usr/local/gromacs/share/gromacs/top':
2: AMBER03 force field (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 force field (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 force field (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB force field (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN force field (Lindorff-Larsen et al., Proteins 78,
1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (with CMAP) - version 2.0
10: CHARMM36 all-atom force field (with CMAP)
11: GROMOS96 43a1 force field
12: GROMOS96 43a2 force field (improved alkane dihedrals)
13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
17: [DEPRECATED] Encad all-atom force field, using full solvent charges
18: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum
charges
19: [DEPRECATED] Gromacs force field (see manual)
20: [DEPRECATED] Gromacs force field with hydrogens for NMR
1
Using the Amber03 force field in directory ./amber03.ff
Opening force field file ./amber03.ff/watermodels.dat
Select the Water Model:
1: TIP3P TIP 3-point, recommended
2: TIP4P TIP 4-point
3: TIP4P-Ew TIP 4-point optimized with Ewald
4: SPC simple point charge
5: SPC/E extended simple point charge
6: None
1
Opening force field file ./amber03.ff/aminoacids.r2b
Opening force field file ./amber03.ff/dna.r2b
Opening force field file ./amber03.ff/rna.r2b
Reading test.pdb...
Read 'Good gRace! Old Maple Actually Chews Slate', 115 atoms
Analyzing pdb file
Splitting PDB chains based on TER records or changing chain id.
There are 1 chains and 0 blocks of water and 6 residues with 115 atoms
chain #res #atoms
1 'A' 6 115
All occupancies are one
Opening force field file ./amber03.ff/atomtypes.atp
Atomtype 1
Reading residue database... (amber03)
Opening force field file ./amber03.ff/aminoacids.rtp
Residue 93
Sorting it all out...
Opening force field file ./amber03.ff/dna.rtp
Residue 110
Sorting it all out...
Opening force field file ./amber03.ff/rna.rtp
Residue 126
Sorting it all out...
Opening force field file ./amber03.ff/aminoacids.hdb
Opening force field file ./amber03.ff/dna.hdb
Opening force field file ./amber03.ff/rna.hdb
Opening force field file ./amber03.ff/aminoacids.n.tdb
Opening force field file ./amber03.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.21#
Processing chain 1 'A' (115 atoms, 6 residues)
There are 0 donors and 0 acceptors
There are 0 hydrogen bonds
Identified residue DT1 as a starting terminus.
Identified residue DC6 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Opening force field file ./amber03.ff/aminoacids.arn
Opening force field file ./amber03.ff/dna.arn
Opening force field file ./amber03.ff/rna.arn
Checking for duplicate atoms....
Now there are 6 residues with 182 atoms
Making bonds...
WARNING: atom H3T is missing in residue DC 6 in the pdb file
You might need to add atom H3T to the hydrogen database of building
block DC3
in the file dna.hdb (see the manual)
There were 1 missing atoms in molecule DNA_chain_A
Number of bonds was 192, now 192
Generating angles, dihedrals and pairs...
Before cleaning: 466 pairs
Before cleaning: 496 dihedrals
Keeping all generated dihedrals
Making cmap torsions...There are 496 dihedrals, 36 impropers, 345 angles
448 pairs, 192 bonds and 0 virtual sites
Total mass 1744.076 a.m.u.
Total charge -6.268 e
Writing topology
Back Off! I just backed up posre.itp to ./#posre.itp.1#
Writing coordinate file...
--------- PLEASE NOTE ------------
You have successfully generated a topology from: test.pdb.
The Amber03 force field and the tip3p water model are used.
--------- ETON ESAELP ------------
gcq#67: "The Wheels On the Bus Go Round and Round" (J. Richman)
On Fri, Jul 8, 2011 at 5:48 AM, <gmx-users-request at gromacs.org> wrote:
> Send gmx-users mailing list submissions to
> gmx-users at gromacs.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> or, via email, send a message with subject or body 'help' to
> gmx-users-request at gromacs.org
>
> You can reach the person managing the list at
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gmx-users digest..."
>
>
> Today's Topics:
>
> 1. Re: Using new atom types (Fabian Casteblanco)
> 2. Re: Re: Using new atom types (Justin A. Lemkul)
> 3. Re: gmx-users Digest, Vol 87, Issue 44 (raghav singh)
> 4. want to remove H5T entry form HDB file / open terminal (P, O)
> for polymerization of i-motif (raghav singh)
> 5. Re: want to remove H5T entry form HDB file / open terminal
> (P, O) for polymerization of i-motif (Justin A. Lemkul)
> 6. Re: Solute potential energy (Mark Abraham)
> 7. help (=?GBK?B?z/7Tog==?=)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 7 Jul 2011 17:32:24 -0400
> From: Fabian Casteblanco <fabian.casteblanco at gmail.com>
> Subject: [gmx-users] Re: Using new atom types
> To: gmx-users at gromacs.org
> Message-ID:
> <CAG3KNbj2A_eUwxrTgm4wcpuxu6hAW_LLVqW4N_VXqqMGf1xr9w at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hello Justin,
>
> Thanks for your help.
>
> Your response:
> No, you need the [defaults] directive from the force field. If you
> want to make
> a completely custom entity, then build your own, although likely most of
> the
> highest-level force field files are going to be the same. You can always
> add a
> new [atomtypes] directive in a proper location in your topology.
>
> Comment: So you are saying I need to refer to the [defaults]
> directive so I need to include {#include "charmm27.ff/forcefield.itp"}
> on my topology file? Below is the [defaults] directive for CHARMM. I
> can simply add my...
>
> >> -CgenFFbon.itp (bonded, angle, dihedral parameters,etc)
> >> -CgenFFnb.itp (nonbonded LJ values)
> >> -CgenFF.atp (atom type file)
>
> to this section?
>
> ****************************************************************
> * Charmm to Gromacs port writted by *
> * Par Bjelkmar, bjelkmar at cbr.su.se *
> * Alternative correspondance: *
> * Erik Lindahl, lindahl at cbr.su.se *
> ****************************************************************
>
>
> #define _FF_CHARMM
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 2 yes 1.0 1.0
>
> #include "ffcharmm27nb.itp"
> #include "ffcharmm27bon.itp"
> **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?
>
> Or would I need to create one almost identical to this except
> replacing the old ffcharm27.itp with my new Cgen.itp files?
>
>
>
> This is my sample topology. Your last statement said I could add
> [atomtypes] to this section. So I can simply include the [defaults]
> directive but just add the Cgenffbon.itp and cCgenffnb.itp to this
> section here?
>
> ;SAMPLE topology:
> ;
> ;
> ; Include forcefield parameters
> #include "charmm27.ff/forcefield.itp"
> **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?
>
> #include "drug.itp"
>
> [ system ]
> ; Name
> DrugName
>
> [ molecules ]
> ; Compound #mols
> DDD 1
>
>
>
> Thanks again for your help. Greatly appreciated!!
>
> Fabian Casteblanco
> Rutgers University
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 07 Jul 2011 17:49:38 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Using new atom types
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E1629F2.8010300 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Fabian Casteblanco wrote:
> > Hello Justin,
> >
> > Thanks for your help.
> >
> > Your response:
> > No, you need the [defaults] directive from the force field. If you
> > want to make
> > a completely custom entity, then build your own, although likely most of
> the
> > highest-level force field files are going to be the same. You can always
> add a
> > new [atomtypes] directive in a proper location in your topology.
> >
> > Comment: So you are saying I need to refer to the [defaults]
> > directive so I need to include {#include "charmm27.ff/forcefield.itp"}
> > on my topology file? Below is the [defaults] directive for CHARMM. I
> > can simply add my...
> >
> >>> -CgenFFbon.itp (bonded, angle, dihedral parameters,etc)
> >>> -CgenFFnb.itp (nonbonded LJ values)
> >>> -CgenFF.atp (atom type file)
> >
> > to this section?
> >
> > ****************************************************************
> > * Charmm to Gromacs port writted by *
> > * Par Bjelkmar, bjelkmar at cbr.su.se *
> > * Alternative correspondance: *
> > * Erik Lindahl, lindahl at cbr.su.se *
> > ****************************************************************
> >
> >
> > #define _FF_CHARMM
> >
> > [ defaults ]
> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> > 1 2 yes 1.0 1.0
> >
> > #include "ffcharmm27nb.itp"
> > #include "ffcharmm27bon.itp"
> > **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?
> >
>
> No, because the required directives would be out of order and grompp would
> fail
> with a fatal error.
>
> > Or would I need to create one almost identical to this except
> > replacing the old ffcharm27.itp with my new Cgen.itp files?
> >
> >
>
> That depends. If your CgenFF* files are completely independent of the
> CHARMM27
> force field files already built into Gromacs, then yes, you can build
> everything
> from scratch. If you need any of the parameters from the existing CHARMM27
> force field, then you have to include your new parameters.
>
> >
> > This is my sample topology. Your last statement said I could add
> > [atomtypes] to this section. So I can simply include the [defaults]
> > directive but just add the Cgenffbon.itp and cCgenffnb.itp to this
> > section here?
> >
> > ;SAMPLE topology:
> > ;
> > ;
> > ; Include forcefield parameters
> > #include "charmm27.ff/forcefield.itp"
> > **???{ #include add new CgenFFbon.itp and CgenFFnb.itp here? }???** ?
> >
>
> No, this would have the same effect as above. What is weird here is that
> this
> .top uses version 4.5 naming, but the files above appear to be from the
> 4.0.x
> series. Mixing these will probably not work. Be sure to standardize the
> files
> you're using to be consistent with the expectations of the Gromacs version
> you're using.
>
> The bottom line is that you should have a thorough read of Chapter 5 of the
> manual to understand the contents of the topology, from the highest level
> (force
> field) down to the molecule level, in terms of both the required order of
> directives and contents thereof. If the CGenFF parameters do not depend on
> the
> existing implementation, then you're probably better off not messing with
> the
> existing files and just creating your own, styled after the existing force
> field.
>
> -Justin
>
> > #include "drug.itp"
> >
> > [ system ]
> > ; Name
> > DrugName
> >
> > [ molecules ]
> > ; Compound #mols
> > DDD 1
> >
> >
> >
> > Thanks again for your help. Greatly appreciated!!
> >
> > Fabian Casteblanco
> > Rutgers University
>
> --
> ========================================
>
> 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: Thu, 7 Jul 2011 17:52:11 -0400
> From: raghav singh <raghavbioinfo at gmail.com>
> Subject: [gmx-users] Re: gmx-users Digest, Vol 87, Issue 44
> To: gmx-users at gromacs.org
> Message-ID:
> <CAHsfQvCy_T3c0-DXqVHqSRS8B2jx3Z8oExaY=qcmMj=CJWAqiQ at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Justin,
>
> Yeah I have to remove that H from the that position to make my P open to
> contact with the O atom of the next unit.
> ..but if you make some precise suggestion that How can I remove that
> entry..
> because I have tried to remove the entry from .RTP and .HDB files and in
> that case it starts giving me error that H5T is not available in rtp and
> hdb
> entry.
>
> I am just getting crazy with this thing... I am creating tons of DATA but
> NOT even a single thing which I can say a CLOSE SOLUTION... the best I
> found
> what I have posted. :(
>
> Need some serious help.. Passed the files to MY PROFESSOR :)
>
> Raghav
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 4
> Date: Thu, 7 Jul 2011 17:53:35 -0400
> From: raghav singh <raghavbioinfo at gmail.com>
> Subject: [gmx-users] want to remove H5T entry form HDB file / open
> terminal (P, O) for polymerization of i-motif
> To: gmx-users at gromacs.org
> Message-ID:
> <CAHsfQvAO4Ra0ehrbjCj41iWwcc6y2_BFqRE5KaxhJofZ1xKbSQ at mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Justin,
>
> Yeah I have to remove that H from the that position to make my P open to
> contact with the O atom of the next unit.
> ..but if you make some precise suggestion that How can I remove that
> entry..
> because I have tried to remove the entry from .RTP and .HDB files and in
> that case it starts giving me error that H5T is not available in rtp and
> hdb
> entry.
>
> I am just getting crazy with this thing... I am creating tons of DATA but
> NOT even a single thing which I can say a CLOSE SOLUTION... the best I
> found
> what I have posted. :(
>
> Need some serious help.. Passed the files to MY PROFESSOR :)
>
> Raghav
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL:
> http://lists.gromacs.org/pipermail/gmx-users/attachments/20110707/1453c323/attachment-0001.html
>
> ------------------------------
>
> Message: 5
> Date: Thu, 07 Jul 2011 18:09:06 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] want to remove H5T entry form HDB file / open
> terminal (P, O) for polymerization of i-motif
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E162E82.9000600 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> raghav singh wrote:
> > Hi Justin,
> >
> > Yeah I have to remove that H from the that position to make my P open to
> > contact with the O atom of the next unit.
> > ..but if you make some precise suggestion that How can I remove that
> > entry.. because I have tried to remove the entry from .RTP and .HDB
> > files and in that case it starts giving me error that H5T is not
> > available in rtp and hdb entry.
>
> You've not shown any evidence that anything you've tried should have even
> worked, for several reasons:
>
> 1. Your .pdb file contains a residue named DT, but your .rtp entries have
> never
> matched that name. pdb2gmx will not match these entries if they do not
> have the
> same name.
>
> 2. The .rtp and .hdb entries you've shown previously specify that H5T
> should be
> there, or otherwise built on. If you properly remove all references to H5T
> (and
> then consequently re-calculate the charges on the associated functional
> groups),
> then there is no way pdb2gmx will try to place the atom there. It simply
> can't.
>
> If you've gotten some error message, please copy and paste it rather than
> trying
> to interpret what you're seeing.
>
> >
> > I am just getting crazy with this thing... I am creating tons of DATA
> > but NOT even a single thing which I can say a CLOSE SOLUTION... the best
> > I found what I have posted. :(
> >
> > Need some serious help.. Passed the files to MY PROFESSOR :)
> >
>
> I understand that everyone has urgent problems to solve, including the
> people
> trying to give of their time to help you. If you've gotten yourself in a
> bind,
> then I can't help that. You've not yet posted any evidence of anything
> that
> might actually accomplish your goal.
>
> -Justin
>
> --
> ========================================
>
> 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: 6
> Date: Fri, 08 Jul 2011 08:16:42 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Solute potential energy
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E16304A.6060101 at anu.edu.au>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
> On 8/07/2011 1:06 AM, Francesco Musiani wrote:
> > Dear Gromacs users,
> > I have the following problem: I need to calculate the potential energy
> > of a protein surrounded by explicit water.
> > In particular, I need to calculate the bond, angle, proper dihedral and
> > improper dihedral terms of potential energy for the solute protein only.
> > How can I extract this values from a trajectory?
>
> Cunning use of mdrun -rerun makes this fairly easy to achieve. Use
> trjconv and tpbconv to create subsets to rerun, IIRC. Search the
> archives for details.
>
> Mark
>
>
> ------------------------------
>
> Message: 7
> Date: Fri, 8 Jul 2011 11:31:59 +0800 (CST)
> From: =?GBK?B?z/7Tog==?= <xiaoyingw11 at 163.com>
> Subject: [gmx-users] help
> To: gmx-users at gromacs.org
> Message-ID: <5fbb45b0.12ca3.13107cd4a76.Coremail.xiaoyingw11 at 163.com>
> Content-Type: text/plain; charset="gbk"
>
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>
> --
> gmx-users mailing list
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> Please search the archive at
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> End of gmx-users Digest, Vol 87, Issue 49
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