[gmx-users] (no subject)

[Justin Lemkul]

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 <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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-- 
==================================================

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================