[gmx-users] No such moleculetype SOL
I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] No such moleculetype SOL
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury jsab...@gmail.com wrote: I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. Have a look at how Justin's tutorial's .top gets access to a water topology. Mark I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reverse_MICELLEFatel error, moleculetype SOL is redefined
On 7/16/13 1:02 AM, Hari Pandey wrote: Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER. When I do grompp, it says moleculetype SOL is redefined and lots of another errors. Please advice me how do I do reverse micelle simulation. What I did is:: (1) pdb2gmx -f RM.pdb -o RM.gro -p RM.top step I choose isooctane as water model. I have isooctane.itp in the file watermodel.dat inside my forcefield. (2) editconf -c -f RM.gro -o RM1.gro -p RM.top -bt dodecahedron -d 2.0 -shell 0.3 (3) genbox -cp RM.gro -cs isooctane.gro -p reverse_RM.top -o RM2.pdb (4) grompp -f em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5 where RM.pdb is pdb file of reverse micelle All required files I have ,and I have index.ndx file also But it returns : Fatel error: the moleculetype SOL is redefined I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit. So You have two topologies that define a [moleculetype] named SOL, which causes the error. Likely it's somewhere in the isooctane.itp file, because you seem to be treating it like water above (which is unnecessary). -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Reverse_MICELLEFatel error, moleculetype SOL is redefined
Hi Gromaxers, Thanks for previous answers. I have to simulate reverse micelle after solvation with isooctane.My system now is: ISOOCTANE(solvent)+AOT(surfactant)+coreWATER. When I do grompp, it says moleculetype SOL is redefined and lots of another errors. Please advice me how do I do reverse micelle simulation. What I did is:: (1) pdb2gmx -f RM.pdb -o RM.gro -p RM.top step I choose isooctane as water model. I have isooctane.itp in the file watermodel.dat inside my forcefield. (2) editconf -c -f RM.gro -o RM1.gro -p RM.top -bt dodecahedron -d 2.0 -shell 0.3 (3) genbox -cp RM.gro -cs isooctane.gro -p reverse_RM.top -o RM2.pdb (4) grompp -f em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5 where RM.pdb is pdb file of reverse micelle All required files I have ,and I have index.ndx file also But it returns : Fatel error: the moleculetype SOL is redefined I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit. So Please advice me how do I do this. Thanks for your help. Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] No such moleculetype SOL
Dear GMX Users, I solve sample in the water, but when I run GROMPP, this error appeares: Fatal error: No such moleculetype SOL Without water, the grompp was done. Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype SOL
- Original Message - From: nanogroup nanogr...@ymail.com Date: Wednesday, July 7, 2010 18:16 Subject: [gmx-users] No such moleculetype SOL To: gmx-users-requ...@gromacs.org Cc: gmx-users@gromacs.org --- | Dear GMX Users, I solve sample in the water, but when I run GROMPP, this error appeares: Fatal error: No such moleculetype SOL Without water, the grompp was done. So you haven't solvated properly, because you have added solvent coordinates, but have no solvent [moleculetype] present in your .top. However, since you haven't provided any details about how you were trying to solvate, you have made it hard to help you. Mark | --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] No such moleculetype SOL
Dear Mark, Many thanks for your e-mail. I checked the TOP file, the SOL is diefined there and numbers of solvent moelcules are presented. I solved the sample by genbox command and selected spc216.gro I am looking forward to reading from you. Bests, Mahmoud -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype SOL
nanogroup wrote: Dear Mark, Many thanks for your e-mail. I checked the TOP file, the SOL is diefined there and numbers of solvent moelcules are presented. If this were true, you wouldn't have gotten the error you did. The best information you can provide is the relevant section of .top file that demonstrates all of this. Perhaps there is a typographical or formatting error that you're not seeing. -Justin I solved the sample by genbox command and selected spc216.gro I am looking forward to reading from you. Bests, Mahmoud -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] No such moleculetype SOL
- Original Message - From: nanogroup nanogr...@ymail.com Date: Wednesday, July 7, 2010 21:51 Subject: [gmx-users] No such moleculetype SOL To: gmx-users@gromacs.org Cc: mark.abra...@anu.edu.au --- | Dear Mark, Many thanks for your e-mail. I checked the TOP file, the SOL is diefined there and numbers of solvent moelcules are presented. I solved the sample by genbox command and selected spc216.gro I've lost count of the number of times in the last three days I've asked people to provide their actual input and output. See the advice here - http://www.gromacs.org/Support Mark | --- -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: moleculetype SOL is redefined.
Hi gromaxers, I want to generate a tpr file for a minimization. I have 3 peptides in water and Im using OPLS ff, but after I run grompp, system backs me the next message: -- creating statusfile for 1 node... checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_X 1 Cleaning up temporary file gromppDDYIem --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 887 Fatal error: moleculetype SOL is redefined -- Some commentary will be very appreciated. Thank you for advance. Dr. Absalom Zamorano Carrillo Profesor Titular A Programa Institucional de Biomedicina Molecular, ENMyH-IPN Guillermo Massieu Helguera #239 Fracc. La Escalera Ticomán, D.F. México, C.P 07320 Tel. (55) 57296000, ext 55542 ___ Do You Yahoo!? La mejor conexión a Internet y b 2GB/b extra a tu correo por $100 al mes. http://net.yahoo.com.mx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Fatal error: moleculetype SOL is redefined.
Hi gromaxers, I want to generate a tpr file for a minimization. I have 3 peptides in water and Im using OPLS ff, but after I run grompp, system backs me the next message: -- creating statusfile for 1 node... checking input for internal consistency... calling /lib/cpp... processing topology... Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours for Protein_X 1 Cleaning up temporary file gromppDDYIem --- Program grompp, VERSION 3.3 Source code file: toppush.c, line: 887 Fatal error: moleculetype SOL is redefined -- Some commentary will be very appreciated. Thank you for advance. Dr. Absalom Zamorano Carrillo Profesor Titular A Programa Institucional de Biomedicina Molecular, ENMyH-IPN Guillermo Massieu Helguera #239 Fracc. La Escalera Ticomán, D.F. México, C.P 07320 Tel. (55) 57296000, ext 55542 ___ Do You Yahoo!? La mejor conexión a Internet y b 2GB/b extra a tu correo por $100 al mes. http://net.yahoo.com.mx ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Fatal error: moleculetype SOL is redefined.
Absalom Zamorano wrote: Strangely enough, the problem is here: Fatal error: moleculetype SOL is redefined Find where moleculetype SOL is defined in your .top file - perhaps implicitly through an #include - and you should see it defined more than once. Evidently you can't do this :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
