[gmx-users] Error with moleculetype

[Justin Lemkul]

On 5/19/17 6:03 PM, Pandya, Akash wrote:
> Tried to put it at the end but it still came up with the same error.
>
> Justin, I don't understand what you mean?
>

If the file has been edited with a non-plain text editor then you can have 
malformed return characters.  Make sure you only ever edit files with vim, 
emacs, etc. and if you're using any Windows-specific editors, process files with 
dos2unix.

-Justin

> Akash
>
> -----Original Message-----
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
> Sent: 19 May 2017 22:35
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Error with moleculetype
>
>
>
> On 5/19/17 5:33 PM, Mark Abraham wrote:
>> Hi,
>>
>> Ok. Maybe it needs to be last in the molecules?
>>
>
> Or perhaps the error points to a malformed line ending that causes genion to choke when updating the topology.
>
> -Justin
>
>> Mark
>>
>> On Fri, 19 May 2017 23:19 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
>>
>>> It was the genion command. Here is the message.
>>>
>>> Fatal error:
>>> No line with moleculetype 'SOL' found the [ molecules ] section of
>>> file 'topol.top'
>>>
>>> -----Original Message-----
>>> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
>>> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark
>>> Abraham
>>> Sent: 19 May 2017 21:26
>>> To: gmx-users at gromacs.org; gromacs.org_gmx-users at maillist.sys.kth.se
>>> Subject: Re: [gmx-users] Error with moleculetype
>>>
>>> Hi,
>>>
>>> I don't think grompp can issue that message. What was the message you
>>> copied and pasted from your terminal?
>>>
>>> Mark
>>>
>>> On Fri, 19 May 2017 18:49 Pandya, Akash <akash.pandya.15 at ucl.ac.uk> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I have received an error message shown below.
>>>>
>>>> Fatal error:
>>>> No line with moleculetype 'SOL' found the [ molecules ] section of
>>>> file 'topol.top'
>>>>
>>>> For more information and tips for troubleshooting, please check the
>>>> GROMACS website at http://www.gromacs.org/Documentation/Errors
>>>>
>>>> I don't understand what's wrong with my topol.top file. I have
>>>> included the following before the [ molecules ] section.
>>>>
>>>> [ moleculetype ]
>>>> ; Name
>>>> SOL                 1
>>>>
>>>> My [ molecules ] section looks like this:
>>>>
>>>> [ molecules ]
>>>> ; Compound        #mols
>>>> Protein_chain_H     1
>>>> SOL             73337
>>>> Citrate            29
>>>> GLY               984
>>>>
>>>>
>>>> I have read the documentation and still don't understand. Please can
>>>> you advise me on what to do?
>>>>
>>>> Many thanks,
>>>> Akash
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
>>>> or send a mail to gmx-users-request at gromacs.org.
>>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
>

-- 
==================================================

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

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