[gmx-users] (no subject)

[Sanim Rahman]

Hi Justin,

I completely dazed over the "download .tgz" option at the top right of the
screen. I got all of the files I need for my membrane. Thank you!

*Sanim Rahman*


On Sat, Mar 18, 2017 at 8:03 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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>
>>> --
>>> Gromacs Users mailing list
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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
>
> ==================================================
>
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