Re: [gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff
On 11/26/16 2:41 PM, Jonathan Phillips wrote: Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27 forcefield that comes with gromacs. FWIW, we have a complete CHARMM36 + latest CGenFF available at our website to save you some pain: http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs pdb2gmx runs without error, however when I run grompp, I get this: Program grompp, VERSION 5.0.4 Source code file: /var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c, line: 742 Fatal error: Unknown bond_atomtype CG1N1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can't work out what bond_atomtype is, or exactly where I've been stupid. "bond_atomtype" means "an atom type used in a bonded interaction." I've checked that: atomtypes.atp contains the following line CG1N1 12.01100 ; for cyano group (if it's relevant, this was generated by appending the cgen atomtypes file to the charmm atomtypes file). ffcgenbonded.itp contains the following lines (under the [ bondtypes ] section) CG1N1 CG2R61 1 0.1435 288696.0 CG1N1 CG331 1 0.147 334720.0 CG1N1 NG1T1 1 0.118 881150.4 charmm27cgen.ff/forcefield.itp contains #include "ffcgenbonded.itp" topol.top contains #include "./charmm27cgen.ff/forcefield.itp" grompp is being called with -p topol.top All bonds containing a CG1N1 atom in cgen.rtp are to one of the three atomtypes in ffcgenbonded.itp quoted above. Also, my ligand doesn't contain residues that have a CG1N1 atom in them (neither does my protein, surprise, surprise). So I don't know why it's looking at CG1N1, and I don't know why there are issues with this atomtype, and I don't know what a bond_atomtype is, which leaves me rather stuck. Does anybody have any suggestions? The presence of an atom type in the .atp file is not enough. That file is only ever read by pdb2gmx. grompp needs parameters for all those atom types in ffnonbonded.itp. So if it finds a bonded interaction that involves an atom type it doesn't know about (e.g. you have a type in ffbonded.itp but not ffnonbonded.itp, which I bet is the case here) you get a fatal error. -Justin -- == 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.
Re: [gmx-users] The time need for each window in umbrella sampling
Hi, Thanks for the answer! Regards, Farideh On Sat, Nov 26, 2016 at 11:37 PM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > block averaging or perhaps reverse cumulative averaging > http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1638996 > (though the later will probably be a pain with PMFs). > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of faride > badalkhani > Sent: 26 November 2016 04:50:29 > To: gmx-us...@gromacs.org > Subject: [gmx-users] The time need for each window in umbrella sampling > > Dear Gromacs users, > > Is there any criteria tk determine tge optimum run time for each window in > umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I > consider the same run time for each window? > > Regards, > Farideh > -- > 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.
Re: [gmx-users] Removal of Waters in Hydrophobic Core
I have not run that in a long time, but looking at it (and my initial post
here:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2006-May/021526.html
) it seems like I wrote out the instructions incorrectly. Sorry about that!
In the post linked above, step 8 is:
cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
but I think you would really want to do this:
cat not_last_line.gro keep_these_waters.gro last_line.gro > new_system.gro
where the change is to *actually use* the keep_these_waters.gro file that we
create with the script ;)
Looks like I realized that a number of years ago:
http://www.mail-archive.com/gmx-users@gromacs.org/msg37736.html
Sorry for the confusion, indeed the commands listed on the webpage seem like
they should lead you to recover exactly the initial file :(
Note also that you need to set the upper and lower bounds correctly, and modify
the script as noted if you are using a 4-point (or 5-ponit) water model, and
make the noted change if your input file has also velocities. All of those
things are correctly indicated on the webpage though.
Please reply back to this list if that change works for you as expected and
I'll bring it to Mark's attention to see if he can update the webpage.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Sanim Rahman
Sent: 26 November 2016 02:18:09
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Removal of Waters in Hydrophobic Core
Thank you Chris,
I tried the commands and I was able to obtain an output
keep_these_waters.gro with about 3.5 MB of data. However, when I continued
with the rest of the commands:
tail -1 initial.gro > last_line.gro
head -$(expr $(cat initial.gro | wc -l | awk '{print $1}') - 1 )
initial.gro > not_last_line.gro
cat not_last_line.gro new_waters.gro last_line.gro > new_system.gro
editconf -f new_system.gro -o new_system_sequential_numbers.gro
I still failed to obtain a new structure. The structure is the same as
solvated.gro. I am going to put extreme z-coordinates to see if all the
water molecules will be removed. Other than that, do you have any
suggestions?
*Sanim Rahman*
B.S. Chemical Engineering, 2019
Undergraduate Researcher, Global Center for Hearing and Speech Research
On Fri, Nov 25, 2016 at 3:48 PM, Christopher Neale <
chris.ne...@alum.utoronto.ca> wrote:
> not sure if it is a typo or perhaps a command structure I am unfamiliar
> with, but I don't understand your command.
>
> Try this:
>
> chmod +x keepbyz.pl
> ./keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> see here: http://www.gromacs.org/Documentation/How-tos/
> Membrane_Simulations?highlight=generates
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Sanim
> Rahman
> Sent: 24 November 2016 16:12:11
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: [gmx-users] Removal of Waters in Hydrophobic Core
>
> Hello,
>
> I am currently working through the second tutorial of the Bevan Labs KALP15
> simulation. I am attempting to use the keepbyz.pl script to remove the
> waters in the hydrophobic core. I have designated a upperz and
> lowerz coordinated and followed the entire section highlighted in the
> instructions, however, my output (new_system_sequential_numbers.gro) has
> no
> deleted water molecules. It is the same system as solvated.gro.
>
> I believe my error is within the keepbyz.pl file, because when I input the
> command:
>
> chmod +x keepbyz.pl new_waters.gro > keep_these_waters.gro
>
> the file "keep_these_waters.gro" is an empty file.
>
> Here is my script for keepbyz.pl:
>
> #!/bin/bash
> # give new_waters.gro as first command line arguement
> upperz=5.821
> lowerz=0.574
> sol=SOL
> count=0
> cat $1 | grep "$sol" | while read line; do
> for first in $line; do
> break
> done
> if [ "$count" = 3 ]; then
> count=0
> fi
> count=$(expr $count + 1)
> if [ "$count" != 1 ]; then
> continue
> fi
> l=${#line}
> m=$(expr $l - 24) // would use -48 if velocities are also in .gro and
> -24 otherwise
> i=1
> for word in ${line:$m}; do
> if [ "$i" = 1 ]; then
> popex=$word
> else
> if [ "$i" = 2 ]; then
> popey=$word
> else
> if [ "$i" = 3 ]; then
> popez=$word
> break
> fi
> fi
> fi
> i=$(expr $i + 1)
> done
> nolx=`echo "$popez > $upperz" | bc`
> nohx=`echo "$popez < $lowerz" | bc`
> myno=$(expr $nolx + $nohx)
> if [ "$myno" != 0 ]; then
> z=${#first}
> if [ "$z" != 8 ]; then
> sfirst="[[:space:]]$first"
> else
> sfirst=$first
> fi
> `echo grep $sfirst $1`
> fi
> done
>
> I will appreciate the help!
>
> Regards,
>
> *Sanim Rahman*
> B.S. Chemical Engineering, 2019
> Resident Assistant, Castor Hall Engineering Living Learning Community
> 2016-2017
> Undergraduat
Re: [gmx-users] The time need for each window in umbrella sampling
block averaging or perhaps reverse cumulative averaging http://scitation.aip.org/content/aip/journal/jcp/120/6/10.1063/1.1638996 (though the later will probably be a pain with PMFs). From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of faride badalkhani Sent: 26 November 2016 04:50:29 To: gmx-us...@gromacs.org Subject: [gmx-users] The time need for each window in umbrella sampling Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- 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.
[gmx-users] Unknown bond_atomtype when trying to use charm27 with cgenff
Hi, I'm trying to run a simulation of a protein:ligand complex using chamm27 and cgenff2b7. After a little hacking (I'm using a PRES), I've used charmm2gromacs-pvm.py to convert cgenff2b7 to cgenff2b7.ff/, and then combined that with the charmm27 forcefield that comes with gromacs. pdb2gmx runs without error, however when I run grompp, I get this: >Program grompp, VERSION 5.0.4 >Source code file: /var/tmp/portage/sci-chemistry/gromacs-5.0.4/work/gromacs-5.0.4/src/gromacs/gmxpreprocess/toppush.c, line: 742 > >Fatal error: >Unknown bond_atomtype CG1N1 > >For more information and tips for troubleshooting, please check the GROMACS >website at http://www.gromacs.org/Documentation/Errors I can't work out what bond_atomtype is, or exactly where I've been stupid. I've checked that: atomtypes.atp contains the following line >CG1N1 12.01100 ; for cyano group (if it's relevant, this was generated by appending the cgen atomtypes file to the charmm atomtypes file). ffcgenbonded.itp contains the following lines (under the [ bondtypes ] section) >CG1N1 CG2R61 1 0.1435 288696.0 >CG1N1 CG331 1 0.147 334720.0 >CG1N1 NG1T1 1 0.118 881150.4 charmm27cgen.ff/forcefield.itp contains >#include "ffcgenbonded.itp" topol.top contains >#include "./charmm27cgen.ff/forcefield.itp" grompp is being called with -p topol.top All bonds containing a CG1N1 atom in cgen.rtp are to one of the three atomtypes in ffcgenbonded.itp quoted above. Also, my ligand doesn't contain residues that have a CG1N1 atom in them (neither does my protein, surprise, surprise). So I don't know why it's looking at CG1N1, and I don't know why there are issues with this atomtype, and I don't know what a bond_atomtype is, which leaves me rather stuck. Does anybody have any suggestions? -- 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.
Re: [gmx-users] setting up a pull vec
Hello Christopher, I have restrained the protein chain and ligand during previous NPT equilibration step(10ns). Is it still possible that the structure will scatter all over if we start pulling ? I want to pull the ligand out of the binding site of this protein and collect intermediary conformers during the process to study the concerned structural changes. Please give me some advice regarding the process. Thanks. On Sat, Nov 26, 2016 at 8:04 AM, Christopher Neale < chris.ne...@alum.utoronto.ca> wrote: > You haven't told us what you want to do, but perhaps you want to pull them > apart along the vector that connects the centers of mass of these two > species. One possible way to do that is to use gmx traj -com to get the two > centers of mass, then figure out the vector yourself. That's going to get > messy if the whole complex tumbles in solution, so you could also add a few > absolute position restraints to pin down one of the molecules. > > > From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of abhisek > Mondal > Sent: 25 November 2016 02:37:18 > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] setting up a pull vec > > Hi, > > I'm trying to run a umbrella sampling using following pull code: > ; Pull code > pull= yes > pull_ngroups= 2 > pull_ncoords= 1 > pull_group1_name= JZ4 > pull_group2_name= Protein_chain_A > pull_coord1_type= umbrella ; harmonic biasing force > pull_coord1_geometry= direction-periodic > pull_coord1_groups = 1 2 > pull_coord1_dim = Y Y Y ; pulling in all dimension > pull_coord1_rate= 0.01 ; 0.01 nm per ps = 10 nm per ns > pull_coord1_k = 500 ; kJ mol^-1 nm^-2 > pull_coord1_start = yes ; define initial COM distance > 0 > > This approach needs me to specify a pulling vec which is essentially not > 0,0,0. > > Could you please suggest me a way to decide how to provide the pull vec ? > > Thanks. > > -- > Abhisek Mondal > > *Research Fellow* > > *Structural Biology and Bioinformatics Division* > *CSIR-Indian Institute of Chemical Biology* > > *Kolkata 700032* > > *INDIA* > -- > 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. > -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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.
[gmx-users] LJ wall
Dear Gromacs users , How Can i change lennard-jones wall s location at Z direction ? I use lennard jones wall with these command in mdp file : ... pbc = xy nwall= 2 wall-atomtype = opls_740 opls_740 wall-type = 9-3 wall-density = 50 50 wall-r-linpot= 1 ... But I get lost atom error , I think it's because of some atoms that are beyond wall ! Can you please let me know How i can change the wall location in system ? Best , Saeed. -- 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.
[gmx-users] The time need for each window in umbrella sampling
Dear Gromacs users, Is there any criteria tk determine tge optimum run time for each window in umbrella sampling? My receptor has equilibrated after 30 ns of MD. Should I consider the same run time for each window? Regards, Farideh -- 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.
Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )
Dear David van der Spoel Thank you for giving me advice. I'll choose TIP4P/Ice model and write its parameters on the topology files. Sincerely. Keisuke Ohki, senior student. Dept. applied physics and physico-informatics., Keio University. -- 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.
Re: [gmx-users] topolbuild ( Failing to read oxygen in H2O )
On 26/11/16 09:24, 大木啓輔 wrote:
Dear gromacs users
I have a question why topolbuild fails to read oxygen in H2O.
I want to make a topology file of methane hydrate structure with topolbuild and
run simulation in gromacs.
For these simple molecules you want hand-tuned force fields not
automatically generated stuff. That mean writing the topologies your
self, and choosing a standard water model, e.g. TIP4P or TIP4P/Ice for
your application.
I used following command line:
./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
.mol2 file that I used then {
@MOLECULE
ch4h2o_4.pdb
46 36 10 0 0
SMALL
USER_CHARGES
@ATOM
1 C 5.60601.66705.1720 C.3 1 LIG1 -0.4588
2 H 6.23902.29905.8040 H 1 LIG10.1147
3 H 4.97401.03505.8040 H 1 LIG10.1147
4 H 4.97402.29904.5400 H 1 LIG10.1147
5 H 6.23901.03504.5400 H 1 LIG10.1147
:
41 O 7.00601.71508.9340 O.3 9 H2O-1.1794
42 H 6.01301.71509.0510 H 9 H2O 0.5897
43 H 7.44401.71509.8330 H 9 H2O 0.5897
44 O 6.95701.72001.4090 O.3 10 H2O-1.1794
45 H 7.20500.87801.8880 H10 H2O 0.5897
46 H 7.24002.50801.9570 H10 H2O 0.5897
@BOND
112 1
213 1
314 1
415 1
:
33 41 42 1
34 41 43 1
35 44 45 1
36 44 46 1
@SUBSTRUCTURE
1 LIG1 1 RESIDUE 4 A LIG1 0 ROOT
2 LIG1 6 RESIDUE 4 A LIG1 0 ROOT
3 LIG111 RESIDUE 4 A LIG1 0 ROOT
4 LIG116 RESIDUE 4 A LIG1 0 ROOT
5 LIG121 RESIDUE 4 A LIG1 0 ROOT
6 LIG126 RESIDUE 4 A LIG1 0 ROOT
7 LIG131 RESIDUE 4 A LIG1 0 ROOT
8 LIG136 RESIDUE 4 A LIG1 0 ROOT
9 H2O41 RESIDUE 4 A H2O 0 ROOT
10 H2O44 RESIDUE 4 A H2O 0 ROOT
}
( this file was used for trial, so this is not hydrate structure )
Then, I got this topology file {
; The force field files to be included
#include "ffHYDRATE_A.itp"
[ moleculetype ]
; name nrexcl
ch4h2o_4.pdb 3
[ atoms ]
; nrtype resnr residu atom cgnrcharge mass
1opls_138 1 LIG C1 -0.45880 12.01100 ;
-0.4588000
2opls_140 1 LIG H1 0.11470 1.00800 ;
-0.3441000
3opls_140 1 LIG H1 0.11470 1.00800 ;
-0.2294000
4opls_140 1 LIG H1 0.11470 1.00800 ;
-0.1147000
5opls_140 1 LIG H1 0.11470 1.00800 ;
0.000
:
41 O?? 9 H2O O9 -1.17940 15.99940 ;
-1.1794000
42opls_435 9 H2O H 10 0.58970 1.00800 ;
-0.5897000
43opls_435 9 H2O H 11 0.58970 1.00800 ;
0.000
44 O??10 H2O O 12 -1.17940 15.99940 ;
-1.1794000
45opls_43510 H2O H 13 0.58970 1.00800 ;
-0.5897000
46opls_43510 H2O H 14 0.58970 1.00800 ;
0.000
; total molecule charge = 0.000
[ bonds ]
; ai aj funct b0 kb
1 2 1 0.10900 284512. ; C- H
1 3 1 0.10900 284512. ; C- H
1 4 1 0.10900 284512. ; C- H
1 5 1 0.10900 284512. ; C- H
:
4142; O- H
4143; O- H
4445; O- H
4446; O- H
[ pairs ]
[ angles ]
; ai aj ak funct th0 cth
3 1 2 1 107.800276.1440 ; H- C- H
4 1 2 1 107.800276.1440 ; H- C- H
5 1 2 1 107.800276.1440 ; H- C- H
:
434142 ; H- O- H
464445 ; H- O- H
}
I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and
H.t3p) ,
but force field types of oxygen in H2O were not read.
Why this problem was occurred?
Should I fix this topology file?
Could you tell me this problem solution, please?
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +4618471
[gmx-users] topolbuild ( Failing to read oxygen in H2O )
Dear gromacs users
I have a question why topolbuild fails to read oxygen in H2O.
I want to make a topology file of methane hydrate structure with topolbuild and
run simulation in gromacs.
I used following command line:
./topolbuild -n ../HYDRATE_A -dir ../dat/gromacs -ff oplsaa -purge 0
.mol2 file that I used then {
@MOLECULE
ch4h2o_4.pdb
46 36 10 0 0
SMALL
USER_CHARGES
@ATOM
1 C 5.60601.66705.1720 C.3 1 LIG1 -0.4588
2 H 6.23902.29905.8040 H 1 LIG10.1147
3 H 4.97401.03505.8040 H 1 LIG10.1147
4 H 4.97402.29904.5400 H 1 LIG10.1147
5 H 6.23901.03504.5400 H 1 LIG10.1147
:
41 O 7.00601.71508.9340 O.3 9 H2O-1.1794
42 H 6.01301.71509.0510 H 9 H2O 0.5897
43 H 7.44401.71509.8330 H 9 H2O 0.5897
44 O 6.95701.72001.4090 O.3 10 H2O-1.1794
45 H 7.20500.87801.8880 H10 H2O 0.5897
46 H 7.24002.50801.9570 H10 H2O 0.5897
@BOND
112 1
213 1
314 1
415 1
:
33 41 42 1
34 41 43 1
35 44 45 1
36 44 46 1
@SUBSTRUCTURE
1 LIG1 1 RESIDUE 4 A LIG1 0 ROOT
2 LIG1 6 RESIDUE 4 A LIG1 0 ROOT
3 LIG111 RESIDUE 4 A LIG1 0 ROOT
4 LIG116 RESIDUE 4 A LIG1 0 ROOT
5 LIG121 RESIDUE 4 A LIG1 0 ROOT
6 LIG126 RESIDUE 4 A LIG1 0 ROOT
7 LIG131 RESIDUE 4 A LIG1 0 ROOT
8 LIG136 RESIDUE 4 A LIG1 0 ROOT
9 H2O41 RESIDUE 4 A H2O 0 ROOT
10 H2O44 RESIDUE 4 A H2O 0 ROOT
}
( this file was used for trial, so this is not hydrate structure )
Then, I got this topology file {
; The force field files to be included
#include "ffHYDRATE_A.itp"
[ moleculetype ]
; name nrexcl
ch4h2o_4.pdb 3
[ atoms ]
; nrtype resnr residu atom cgnrcharge mass
1opls_138 1 LIG C1 -0.45880 12.01100 ;
-0.4588000
2opls_140 1 LIG H1 0.11470 1.00800 ;
-0.3441000
3opls_140 1 LIG H1 0.11470 1.00800 ;
-0.2294000
4opls_140 1 LIG H1 0.11470 1.00800 ;
-0.1147000
5opls_140 1 LIG H1 0.11470 1.00800 ;
0.000
:
41 O?? 9 H2O O9 -1.17940 15.99940 ;
-1.1794000
42opls_435 9 H2O H 10 0.58970 1.00800 ;
-0.5897000
43opls_435 9 H2O H 11 0.58970 1.00800 ;
0.000
44 O??10 H2O O 12 -1.17940 15.99940 ;
-1.1794000
45opls_43510 H2O H 13 0.58970 1.00800 ;
-0.5897000
46opls_43510 H2O H 14 0.58970 1.00800 ;
0.000
; total molecule charge = 0.000
[ bonds ]
; ai aj funct b0 kb
1 2 1 0.10900 284512. ; C- H
1 3 1 0.10900 284512. ; C- H
1 4 1 0.10900 284512. ; C- H
1 5 1 0.10900 284512. ; C- H
:
4142; O- H
4143; O- H
4445; O- H
4446; O- H
[ pairs ]
[ angles ]
; ai aj ak funct th0 cth
3 1 2 1 107.800276.1440 ; H- C- H
4 1 2 1 107.800276.1440 ; H- C- H
5 1 2 1 107.800276.1440 ; H- C- H
:
434142 ; H- O- H
464445 ; H- O- H
}
I tried other input files with changing O.3 to (O.spc and H.spc) and (O.t3p and
H.t3p) ,
but force field types of oxygen in H2O were not read.
Why this problem was occurred?
Should I fix this topology file?
Could you tell me this problem solution, please?
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[gmx-users] The time need fir each window in umbrella sampling
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