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-boun...@maillist.sys.kth.se
[mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Justin
Lemkul
Sent: 19 May 2017 22:35
To: gmx-us...@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...@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-boun...@maillist.sys.kth.se [mailto:
gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Mark
Abraham
Sent: 19 May 2017 21:26
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@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...@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-requ...@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-requ...@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-requ...@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
jalem...@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-requ...@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
jalem...@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-requ...@gromacs.org.
