On 3/18/17 1:25 AM, Sanim Rahman wrote:
Sorry I found this thread here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-September/108197.html
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.
-Justin
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research
<https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
On Sat, Mar 18, 2017 at 12:37 AM, Sanim Rahman <san...@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 =
1,
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"*
*#endif*
*; 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*
*#endif*
*; Include topology for ions*
*#include "./charmm36-nov2016.ff/ions.itp"*
*[ system ]*
*; Name*
*Protein*
*[ 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
error.
Thank you. I will truly appreciate your assistance.
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Resident Assistant, Castor Hall Engineering Living Learning Community
2016-2017
Co-Founder and Co-President of the Undergraduate Research Society
Undergraduate Researcher, Global Center for Hearing and Speech Research
<https://www.linkedin.com/pub/sanim-rahman/108/a64/986>
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