[gmx-users] (no subject)
jalemkul at vt.edu
Sat Mar 18 13:03:49 CET 2017
On 3/18/17 1:25 AM, Sanim Rahman wrote:
> Sorry I found this thread here:
> From my understanding, I use pdb2gmx on my entire output file, however,
> where does the data in the .psf file go?
You shouldn't be using pdb2gmx at all. CHARMM-GUI gives you a complete system
topology that should work, as long as you don't modify anything about the system.
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> Co-Founder and Co-President of the Undergraduate Research Society
> Undergraduate Researcher, Global Center for Hearing and Speech Research
> On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman <sanimr at mail.usf.edu> wrote:
>> Hi all,
>> I am trying to run grompp on POPC lipid bilayer that I constructed in
>> CHARMM-GUI. I originally input the whole assembled bilayer from CHARMM-GUI,
>> however, I received the error:
>> "No Default U-B Types"
>> From a few previous threads, it was suggested that I stripped the waters
>> and use pdb2gmx on them separately in GROMACS. I did that and included the
>> #include command in my lipid topology file to reference water.itp. However,
>> I receive the following error:
>> "Atoms in the .top are not numbered consecutively from 1 (rather, atomnr =
>> while at->nr = 17152)"
>> This is what the end of my POPC topology file looks like:
>> *; Include Position restraint file*
>> *#ifdef POSRES*
>> *#include "posre.itp"*
>> *; Include water chain topology*
>> *#include "water.itp"*
>> *; Include water topology*
>> *#include "./charmm36-nov2016.ff/tip3p.itp"*
>> *#ifdef POSRES_WATER*
>> *; Position restraint for each water oxygen*
>> *[ position_restraints ]*
>> *; i funct fcx fcy fcz*
>> * 1 1 1000 1000 1000*
>> *; Include topology for ions*
>> *#include "./charmm36-nov2016.ff/ions.itp"*
>> *[ system ]*
>> *; Name*
>> *[ molecules ]*
>> *; Compound #mols*
>> *Other 1*
>> *Water 1*
>> I recalled implementing the same technique in one of the GROMACS tutorials,
>> but I am unsure what I am doing differently in my approach to receive this
>> Thank you. I will truly appreciate your assistance.
>> *Sanim Rahman*
>> B.S. Chemical Engineering, 2019
>> Resident Assistant, Castor Hall Engineering Living Learning Community
>> Co-Founder and Co-President of the Undergraduate Research Society
>> Undergraduate Researcher, Global Center for Hearing and Speech Research
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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