[gmx-users] (no subject)

[Sanim Rahman]

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?

*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 <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 =
> 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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