Hi, You should add "-nc" option to your antechamber command, which specifies the net charge of your unit. You can type "antechamber -h" command to get more information.
On 30 September 2016 at 16:47, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You'll probably have better luck getting help with how to use AmberTools > from the AmberTools documentation and the Amber mailing list. And search > Google for that error message first, because it's probably been seen > before. > > Mark > > On Fri, Sep 30, 2016 at 10:44 AM Anu George <g_...@blr.amrita.edu> wrote: > > > Hi everyone, > > I am trying to do a simulation of "RAS G12V - PI 3-KINASE GAMMA COMPLEX" > > which has the ligands 'GNP' and Mg2+. For GNP i tried to create the > > topology by using antechamber giving input as GNP.pdb which was extracted > > from the pdb file (1he8.pdb) but it is giving the error as > > Error: cannot run "/home/anugeorge/amber16/bin/sqm -O -i sqm.in -o > > sqm.out" of bcc() in charge.c properly, exit" when I run the command > > antechamber -i GNP.pdb -fi pdb -fo ac -o GNP.ac -c bcc -s 2 -ek > > grms_tol=0.005 > > > > Please suggest a way to overcome this error" > > Thanks in advance > > Anu George > > > > ----- Original Message ----- > > From: "Dd H" <ddhe...@gmail.com> > > To: gmx-us...@gromacs.org > > Sent: Wednesday, September 21, 2016 6:12:54 PM > > Subject: Re: [gmx-users] parameters of GppNHp > > > > Hi Anu, > > Not very sure what is your trouble. I can figure out two ways to get the > > GppNHp parameters: > > 1). Since GppNHp is very similar to GTP. We can borrow the most of > > parameters from GTP (you can find GTP parameters in AMBER parameter > > database), then derive the rest missing parameters or borrow them from > GAFF > > (I don't know whether it's right to mix them up in a molecule). > > 2). Using GAFF entirely. > > > > Best regards, > > Dading > > > > On 20 September 2016 at 23:54, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 9/19/16 11:18 PM, Anu George wrote: > > > > > >> Hi everyone, > > >> I am also working on simulation a protein-protein complex which has > the > > >> ligand GppNHp molecule and an analogue of GTP. > > >> I tried to build the topology using GAFF and antechamber. but it was > not > > >> working. > > >> Please provide the details for obtaining the same > > >> > > >> > > > You'll have to explain better what exactly you did and what didn't > work. > > > "It was not working" is a useless statement in any scientific field. > > What > > > did you do? What failed? If it's a problem with some external > > > program/server, you need to consult its documentation, FAQs, and > contact > > > its developer(s) for help. If it's a GROMACS problem (specific error > > > message, difficulty putting parameters in the right format, etc) then > > > describe the situation completely. > > > > > > -Justin > > > > > > > > > Dading Huang- if you are able to create the topology and coordinate > file > > >> for the same please share the details > > >> > > >> Thanks in advance > > >> Anu George > > >> > > >> ----- Original Message ----- > > >> From: "Dd H" <ddhe...@gmail.com> > > >> To: gmx-us...@gromacs.org > > >> Sent: Monday, September 19, 2016 6:59:01 AM > > >> Subject: Re: [gmx-users] parameters of GppNHp > > >> > > >> Thank you. I have found a tutorial and I will try to derive them. > > >> > > >> On 19 September 2016 at 00:40, Justin Lemkul <jalem...@vt.edu> wrote: > > >> > > >> > > >>> > > >>> On 9/18/16 3:37 AM, Dd H wrote: > > >>> > > >>> Hi everyone, > > >>>> I want to simulate a protein-ligand complex. The ligand is a GppNHp > > >>>> molecule and an analogue of GTP. I cannot find parameters of GppNHp > in > > >>>> AMBER parameter database (parameters of GTP are supplied there). Can > > you > > >>>> tell me how to get the parameters of GppNHp? Thank you in advance! > > >>>> > > >>>> > > >>>> Derive them in a manner consistent with the parent AMBER force > field. > > >>> There are lots of ways to start going about this, e.g. online > servers, > > >>> GAFF, antechamber, etc. > > >>> > > >>> -Justin > > >>> > > >>> -- > > >>> ================================================== > > >>> > > >>> Justin A. Lemkul, Ph.D. > > >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow > > >>> > > >>> Department of Pharmaceutical Sciences > > >>> School of Pharmacy > > >>> Health Sciences Facility II, Room 629 > > >>> University of Maryland, Baltimore > > >>> 20 Penn St. > > >>> Baltimore, MD 21201 > > >>> > > >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > >>> http://mackerell.umaryland.edu/~jalemkul > > >>> > > >>> ================================================== > > >>> -- > > >>> 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. > > >>> > > >>> > > > -- > > > ================================================== > > > > > > Justin A. Lemkul, Ph.D. > > > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > > > > > Department of Pharmaceutical Sciences > > > School of Pharmacy > > > Health Sciences Facility II, Room 629 > > > University of Maryland, Baltimore > > > 20 Penn St. > > > Baltimore, MD 21201 > > > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > > http://mackerell.umaryland.edu/~jalemkul > > > > > > ================================================== > > > -- > > > 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. > > -- > > 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. > -- 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.