Hi, I don't understand whether you think diglycine is your solvent or your solute.
Mark On Tue, Aug 22, 2017 at 8:40 AM Dilip H N <cy16f01.di...@nitk.edu.in> wrote: > Hello, > 1] it is the solute+Diglycine which is the constituting the mixture... > 2] the method to create the system for both were the same... > the commands are... > gmx editconf -f Diglycinechimera2.gro -o Diglybox.gro -c -box x y z > (generating the box) > gmx insert-molecules -f Diglybox.gro -ci abc.gro -nmol 10 -o Dglyabc.gro > and for other system, gmx insert-molecules -f Diglybox.gro -ci def.gro > -nmol 10 -o Dglydef.gro (adding the solute molecules and getting the final > system)... > here the two solute .gro files are abc.gro and def.gro....and i have > followed the same procedure... > and thn gmx pdb2gmx -f Dglyabc.gro (or) gmx pdb2gmx -f Dglydef.gro...there > is [cmap] option in one topology file and in other topology there is no > [cmap] option... > > How is it different thn..?? > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > < > https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22 > > > > On Tue, Aug 22, 2017 at 11:49 AM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Your description is too confused to follow. Your use of the words solvent > > and solute is unclear. pdb2gmx will never make a cmap that goes outside a > > moleculetype. > > > > If one use of pdb2gmx made a cmap and the other did not, then they were > > fundamentally different. If you don't know what was different, then you > > aren't doing science because you don't know what your method was. If so, > > start again and keep a record in a shell script this time. > > > > Mark > > > > On Tue, Aug 22, 2017 at 8:05 AM Dilip H N <cy16f01.di...@nitk.edu.in> > > wrote: > > > > > 1] in the line 8231 [ Unknown cmap torsion between atoms 8 10 12 15 18] > > it > > > is the diglycine peptide molecule only, it is stating the atomic > numbers > > of > > > the diglycine molecule (8,10,12,15) and solute molecule (18).... > > > 2] but one more problem is the Diglycine nitrogen and the solute > > containing > > > nitrogen are labelled as same (as N only)... > > > ie., atoms 8,10,12,15 (here atom 10 is N, and other atoms are C, CA) > > > belong to diglycine and atom 18 belong to solute molecule of atom N, > and > > > hence i am getting the error...i hope so....(But with other system tht > i > > > ran had no [cmap] in topology and the atoms in the solute were labelled > > > differently....and ran correctly..) > > > 3] So can i remove/delete the [cmap] line .... (i tried removing cmap > > line > > > in topology..and thn with gmx grompp option it is workin fine..) does > > that > > > cause any error/manipulating the topology..etc..?? can i proceed > removing > > > [cmap].... is thr any harm..? > > > 4] I tried also with removing the last coloumn in [cmap] ie., removing > > 18,1 > > > of am,funct..since as i told above the atom 18 is of the solute > nitrogen > > > molecule which is labelled as same in the .rtp file in charmmFF, which > is > > > causing the problems....since the gmx grompp is trying to bond wiht the > > > atom 18 N which is solute and not Diglycine (since both N's are > labelled > > > same) > > > [ cmap ] > > > ; ai aj ak al am funct > > > 8 10 12 15 18 1 > > > and edited and got it as:- > > > > > > [ cmap ] > > > ; ai aj ak al > > > 8 10 12 15 > > > and thn now if i run gmx grompp -f min.mdp -c mixture.gro -p topol.top > -o > > > min.tpr > > > it is showing:- > > > WARNING 1 [file topol.top, line 8231]: > > > Too few parameters on line (source file > > > > > > /home/dilip/Downloads/gromacs-2016.2/src/gromacs/ > > gmxpreprocess/toppush.cpp, > > > line 2198) > > > So i tried with gmx grompp -f min.mdp -c mixture.gro -p topol.top -o > > > min.tpr -maxwarn 2 , and now it is working fine... > > > > > > So i have tried with different options..and i have discussed what i > have > > > got..but are they the correct way...to proceed..?? > > > > > > Any suggestions are welcome... > > > > > > Thank you... > > > > > > > > > <https://mailtrack.io/> Sent with Mailtrack > > > < > > > https://mailtrack.io/install?source=signature&lang=en& > > referral=cy16f01.di...@nitk.edu.in&idSignature=22 > > > > > > > > > > On Mon, Aug 21, 2017 at 11:14 PM, Mark Abraham < > mark.j.abra...@gmail.com > > > > > > wrote: > > > > > > > Hi, > > > > > > > > If your procedure for the two systems was actually the same, then the > > > error > > > > does not come from your solute. Unfortunately only you know what is > on > > > line > > > > 8231... Work out what you did differently, e.g. by doing it again and > > > > making sure you do it the same way. > > > > > > > > Mark > > > > > > > > On Mon, Aug 21, 2017 at 7:27 PM Dilip H N <cy16f01.di...@nitk.edu.in > > > > > > wrote: > > > > > > > > > 1] I created Diglycine peptide from chimera software, and got the > > .pdb > > > > > file, added two different solvents (A, B) and made two different > > > systems > > > > > say, A-(Diglycine+solvent1), B-(Diglycine+solvent2). I generated > the > > > > > topology file from charmm36 FF by gmx pdb2gmx process for both the > > > > systems > > > > > A and B correctly (but in system A there is no [ cmap ] line in > > > topology, > > > > > but system B has [ cmap ] in topology).. Why is this in one system > i > > am > > > > > getting but in other i am not..? Is there any error...or what is > > it... > > > > > > > > > > 2] And during gmx grompp -f min.mdp -c mixture.gro -p topol.top > -o > > > > > min.tpr > > > > > > > > > > for system A (whr there is no [cmap] in topology), the gmx grompp > > > command > > > > > works well... > > > > > But for system B (which has [cmap] in topology), the error comes > as:- > > > > > > > > > > > ERROR 1 [file topol.top, line 8231]: > > > > > > Unknown cmap torsion between atoms 8 10 12 15 18 > > > > > > > > > > How can i solve this ...?? > > > > > > > > > > Thank you... > > > > > > > > > > > > > > > On Mon, Aug 21, 2017 at 10:18 PM, Mark Abraham < > > > mark.j.abra...@gmail.com > > > > > > > > > > wrote: > > > > > > > > > > > Hi, > > > > > > > > > > > > On Mon, Aug 21, 2017 at 6:33 PM Dilip H N < > > cy16f01.di...@nitk.edu.in > > > > > > > > > > wrote: > > > > > > > > > > > > > Hello, > > > > > > > I have created a peptide from chimera software and got the pdb > > > file, > > > > > and > > > > > > i > > > > > > > have added solvents to it the resultant is mixture.gro, and > used > > > gmx > > > > > > > pdb2gmx to generate the topology using charmm36 FF. I got the > > > > topology > > > > > > > correct, but nw if i give the command for energy minimization > :- > > > > > > > gmx grompp -f min.mdp -c mixture.gro -p topol.top -o min.tpr > > > > > > > > > > > > > > I am getting error as:- > > > > > > > > > > > > > > NOTE 1 [file min.mdp]: > > > > > > > With Verlet lists the optimal nstlist is >= 10, with GPUs >= > > 20. > > > > Note > > > > > > > that with the Verlet scheme, nstlist has no effect on the > > > accuracy > > > > of > > > > > > > your simulation. > > > > > > > > > > > > > > Setting the LD random seed to -1490567170 > > > > > > > Generated 97877 of the 97903 non-bonded parameter combinations > > > > > > > Generating 1-4 interactions: fudge = 1 > > > > > > > Generated 64492 of the 97903 1-4 parameter combinations > > > > > > > > > > > > > > ERROR 1 [file topol.top, line 8231]: > > > > > > > Unknown cmap torsion between atoms 8 10 12 15 18 > > > > > > > > > > > > > > There was 1 note > > > > > > > ------------------------------------------------------- > > > > > > > Program: gmx grompp, version 2016.3 > > > > > > > Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1622) > > > > > > > > > > > > > > Fatal error: > > > > > > > There was 1 error in input file(s) > > > > > > > > > > > > > > 1] What is this cmap all about..?? > > > > > > > > > > > > > > > > > > > That's part of how the CHARMM force field works for modelling > > > peptides. > > > > > You > > > > > > should have a basic understanding of that from your background > > > reading > > > > > that > > > > > > led to the choice of this force field. > > > > > > > > > > > > > > > > > > > 2] How do i correct this error..? > > > > > > > > > > > > > > > > > > > Whether you can do so depends whether chimera has generated a > > > structure > > > > > > that has a valid CHARMM36 representation, ie there exists a CMAP > > > > > definition > > > > > > for the types of those atoms. > > > > > > > > > > > > Mark > > > > > > > > > > > > > > > > > > > Any suggestions will be helpful... > > > > > > > > > > > > > > Thank you... > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > With Best Regards, > > > > > > > > > > > > > > DILIP.H.N > > > > > > > Ph.D Student > > > > > > > -- > > > > > > > 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. > > > > > > > > > > > > > -- > > > > > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > With Best Regards, > > > > > > > > > > DILIP.H.N > > > > > Ph.D Student > > > > > -- > > > > > 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. > > > > > > > > > -- > > > > 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. > > > > > > > > > > > > > > > > -- > > > With Best Regards, > > > > > > DILIP.H.N > > > Ph.D Student > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? 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