Re: [gmx-users] Clustering energy minimized equally space frames
> From: gromacs.org_gmx-users-requ...@maillist.sys.kth.se
> Subject: gromacs.org_gmx-users Digest, Vol 134, Issue 66
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Date: Thu, 11 Jun 2015 11:37:49 +0200
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> Today's Topics:
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>1. Clustering energy minimized equally space frames (ashish bihani)
>2. Re: Clustering energy minimized equally space frames
> (Mark Abraham)
>3. energy groups definition (gozde ergin)
>4. problem using grompp (Sotirios Dionysios I. Papadatos)
>5. Re: energy groups definition (gozde ergin)
>6. Crash of DD with periodic_molecules (Semen)
>7. Re: problem using grompp (Mark Abraham)
>
>
> ----------
>
> Message: 1
> Date: Thu, 11 Jun 2015 12:29:48 +0530
> From: ashish bihani
> To: GROMACS users mailing list
> Subject: [gmx-users] Clustering energy minimized equally space frames
> Message-ID:
> Content-Type: text/plain; charset="iso-8859-1"
>
>
>
>
> I extracted [was instructed to extract] trajectory frames at every 10 ps from
> a 10ns xtc file and energy minimized each of them. How do I cluster them?
> I tried to do "ls *.gro | gmx cluster -f {.}.gro ", did not work.
> I concatenated the frames and made an xtc file and tried to cluster it in
> MSMbuilder which did not work. Clustering it in gmx cluster would require a
> tpr file which is not there for this trajectory. What do I do?
>
>
>
> --
>
> Message: 2
> Date: Thu, 11 Jun 2015 07:54:58 +
> From: Mark Abraham
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Clustering energy minimized equally space
> frames
> Message-ID:
>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> On Thu, Jun 11, 2015 at 9:00 AM ashish bihani
> wrote:
>
> >
> >
> >
> > I extracted [was instructed to extract] trajectory frames at every 10 ps
> > from a 10ns xtc file and energy minimized each of them. How do I cluster
> > them?
> > I tried to do "ls *.gro | gmx cluster -f {.}.gro ", did not work.
> >
>
> Unfortunately, the description "did not work" doesn't let us help you fix
> it.
>
>
> > I concatenated the frames and made an xtc file and tried to cluster it in
> > MSMbuilder which did not work. Clustering it in gmx cluster would require a
> > tpr file which is not there for this trajectory. What do I do?
> >
>
> Since you later need a .tpr file for the EM, there's no additional problem.
> If you don't have access to (making) the original .tpr that made the
> simulation, how can anybody reproduce this work?
>
> Mark
>
>
> > --
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#Okay, sorry about that.
#I can't understand how you reply to one particular thread in a mailing list.
Please see if I am doing this correctly this time.
#I have solved my problem. It was a bit bizarre, so here is a summary:
I ran a 10 ns MD simulation (mdrun) and created a .gro file (trjconv) every 10
ps. I minimized (mdrun) each of these files. I needed to cluster these so that
I could look at representative structures from the simulation of the
intermediate.
Now,
1.
"gmx cluster -f *.gro -s run.tpr <<<0" or "ls *.gro | gmx cluster -f {.}.gro -s
run.tpr <<<0" just reads the first .gro file out of the directory that contains
all the frames and stops. It lists all the filenames that ls fed to it. Because
-f takes only one argument here.
2.
I concatenated all these .gro files(trjcat). Th
[gmx-users] Clustering energy minimized equally space frames
I extracted [was instructed to extract] trajectory frames at every 10 ps from a
10ns xtc file and energy minimized each of them. How do I cluster them?
I tried to do "ls *.gro | gmx cluster -f {.}.gro ", did not work.
I concatenated the frames and made an xtc file and tried to cluster it in
MSMbuilder which did not work. Clustering it in gmx cluster would require a tpr
file which is not there for this trajectory. What do I do?
--
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[gmx-users] Format for nonbonded interactions (pairs) in a residue definition
PRODRG has generated force field parameters for Inositol Pyrophosphate (as mentioned in the tutorials). I reformatted atoms, bonds, bond angles, dihedrals and impropers by imitating the format followed in the definitions of other residues in aminoacids.rtp. But I am not able to find a format for [ pairs ].Unlike dihedrals, pairs defined in ffnonbonded file of gromos54A7 have not been assigned codes. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization for Inositol pyrophosphate
Hello, I have understood my mistakes that I reported in previous queries of this string. now, I am proceeding more systematically. I have generated ff parameters for Inositol Pyrophosphate with the help of PRODRG server (as mentioned in the tutorials) as a residue and added it to aminoacids.rtp. I was able to reformat atoms, bonds, bond angles, dihedrals and impropers by imitating the format of the definitions of other residues. But I am not able to find a format for [ pairs ] which I believe is important for my experiment. Particular pairs defined in ffnonbonded.itp file of gromos54A7 do not have codes unlike dihedrals. If I have two columns for individual atoms (e.g. O35 tab P15 tab ?) involved in the interaction, how do I point the program to corresponding c6 and c12 values in ffnonbonded.itp? Secondly, the parameter file generated by PRODRG does not contain all the possible dihedral in Inositokl Pyrophosphate. Are those interactions ignored because of some criteria or should I add them manually? From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: RE: Energy minimization for Inositol pyrophosphate Date: Fri, 30 Jan 2015 12:25:43 +0530 Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two. From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: Energy minimization for Inositol pyrophosphate Date: Thu, 29 Jan 2015 16:53:56 +0530 Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Energy minimization for Inositol pyrophosphate
Hello, I understand that .itp is a topology file. But the swissparam pack does not have a .gro file. How do I create solvated.gro ? (which has to be used in grompp) Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say whether .itp can sustitute the other two. From: ashish.bih...@outlook.com To: gmx-us...@gromacs.org Subject: Energy minimization for Inositol pyrophosphate Date: Thu, 29 Jan 2015 16:53:56 +0530 Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Energy minimization for Inositol pyrophosphate
Hello all, I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the structure from scratch. I have converted PDB to mol2 with openbabel and submitted at Swissparam (http://swissparam.ch/) which returned a zip file containing various files of the same name (.itp, .rtp, .crd, .par, .psf, .pdb, .mol2). 1. Which of these files can be used as force field to generate a topology ? How do I include that file ?pdb2gmx -f IP7270115.pdb -ff XXX -water spc 2. The regular ffs among the options do not recognize IP7 as its atoms can not be associated with protein/DNA/RNA. All the ffs are based on amino acid residues and nucleotides. Is there an atom based ff available for GROMACS which I can place in ff directory and include in ff list ? (like MMFF)Swissparam help page says that I have to change the UNK1/LIG notation in pdb file to CHARMM27 terminology for those atoms. I am having a hard time figuring out what names these atoms should be assigned since all the atoms are unknown. I am attaching the pack returned by swissparam and the version of pdb file with some name modifications.Thank you. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Force field for phosphoserine
Hello everyone,Has anyone subjected a polypeptide containing a phosphoserine residue to :~$ pdb pdb2gmx ? The program does not recognize serine as it has a phosphorus atom attached to it which is not present in the definition. I am trying to define phosphoserine as a residue (let's say PSER). Can anyone tell me what all files do I need to edit (what kind of data do I need to look for, to be more specific) in order to make the program recognize this new residue ?Thanks in advance for help.Regards,Ashish Bihani -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
