[gmx-users] implicit solvent simulation in gromacs

. If it is avilable, could anybody please give me the mdp option. Is it okay to use 43a1 FF? Thanks Chanchal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don&#

Re: [gmx-users] error in converting charmm to gromacs

column corresponding to dihedraltype is 9. But I guess it should be either 1 or 3. I also found that the columns in ffcharmm*.itp are not aligned. Could this be the reason? Thanks Chanchal On Sun, Nov 22, 2009 at 10:12 AM, Chanchal wrote: > Hi Mark, >I need 36 because I am workin

Re: [gmx-users] error in converting charmm to gromacs

les/toppar_carbo_jul_2009.tgz> It would be very helpful to me if you can fix the scripts accordingly. Thanks Chanchal On Fri, Nov 20, 2009 at 8:20 PM, Mark Abraham wrote: > Chanchal wrote: > >> Hi All, >>I want to create ffcharmm*.itp file from par_all36_carb.prm using the >> script pro

[gmx-users] error in converting charmm to gromacs

lication (*) at ./ convert_charmm_to_gromacs.pl line 270, line 1382. Argument "EPS" isn't numeric in multiplication (*) at ./ convert_charmm_to_gromacs.pl line 279, line 1382. How can I fix this error? Thanks Chanchal -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mai

Re: [gmx-users] error in converting charmm to gromacs !!

! Thanks Chanchal On Tue, Sep 29, 2009 at 11:42 AM, Justin A. Lemkul wrote: > > > Chanchal wrote: > >> Hi All, >>I am have built a DOPC+water (tip3p) system in www.charmm-gui.org < >> http://www.charmm-gui.org>. I converted *.itp file from CHARMM *.prm file >

[gmx-users] error in converting charmm to gromacs !!

database But I saw that ffcharmm.rtp (Yuguang Mu's file that I got from Mark Abraham) contains ON2b. So how can I fix this error? Is it problem with ffcharmm.atp? Should I not copy ffcharmm27.atp to ffcharmm.atp? Thanks Chanchal ___ gmx-u

[gmx-users] error in converting charmm to gromacs

help me to fix this error and provide the *.rtp file? Thanks Chanchal ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please

Re: [gmx-users] error while executing grompp

different molecule than you intended to. In that case move the "settles" section to the right molecule. --- Thanks Chanchal On Tue, Aug 25, 2009 at 5:06 PM, Justin A. Lemkul wrote: > > > Chanchal wrote: > >> Hi Justin

Re: [gmx-users] error while executing grompp

Hi Justin, Sorry, I attached the wrong file. Attached is the correct file. Thanks Chanchal On Tue, Aug 25, 2009 at 4:56 PM, Justin A. Lemkul wrote: > > > Chanchal wrote: > >> Hi Justin, >> I am still getting the error message : Back Off! I just backed up >&g

Re: [gmx-users] error while executing grompp

o. In that case move the "settles" section to the right molecule. --- As you said I added the line #define_FF_CHARMM in ffcharmm.itp. Attached is the file. Thanks Chanchal On Tue, Aug 25, 2009 at 4:42 PM, Justin A. Lemkul wrote: > &

[gmx-users] error while executing grompp

ion to the right molecule. --- Attached is the em.mdp file I am using. Please help me how to solve this problem. Thanks Chanchal em.mdp Description: Binary data ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs

Re: [gmx-users] error in residue topology

gromos96 45a3. Will it create problem when we combine sugar /dopc system? Thanks Chanchal On Tue, Aug 18, 2009 at 7:46 PM, Justin A. Lemkul wrote: > > > Chanchal wrote: > >> Hi All, >> I am a novice in gromacs. I want to study sugar/membrane interaction and >> I want to

[gmx-users] error in residue topology

choose gromos96 45a3 force field. But I got the error "Residue 'OLE' not found in residue topology database". How can I fix the error? Thanks Chanchal ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailma