[gmx-users] Re:pdb files and force field

hello sir, Thankyou for the reply. The pdb file i had taken from the TINKER is the one where force field used is oplsaa. when i use this file in gromacs.it give error of atom type. when i had gone in top folder which is in gromacs where all the force fields are defined. its written that you must

[gmx-users] pdb file and force filed

Hello sir, >From last few days , i was using TINKER for implicit simulations using force field oplsaa Now for explicit one, i switched to gromacs version 4.0.But if i take pdb file from tinker (molecular modelling software) and paste it in The Dundee Prodrg server. i got my *.itp file, *.gro file.

[gmx-users] Explicit \ implicit

Hello Everyone, I always use gromacs for doing explicit simulations. I want to ask whether i can do the implicit simulations by using gromacs. Whether there is any tutorial or manual from which i can understand it better. If not, Then Pls tell me how to do it implicitly. With Regards Bhawana

[gmx-users] How to make pdb file of whole trajectory

Hello everyone, Thankyou for the reply for my previous message. But sorry to say I didn't get, what you want to say. Please tell me in elaborated way. I will be thankful. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://ww

[gmx-users] how to make whole trajectory Pdb files

Hello Everyone, Pls tell me after doing simulation, which command should i use ,so that i can get all the pdb files of whole trajectory. I know the command where i can get one pdb file at a time, i.e. trjconv -f *_vac_md_1ns.xtc -s *_vac_md_1ns.tpr -dt 20 -b 0 -e 300 -o _vac_md_1ns_300.pdb trjconv

[gmx-users] two peptides in same water box

Hello everyone, pls tell me that how should i do dimerization. i.e. i want to put two peptides in same water box, but i am not getting of how to do it. Please help me out. With Regards Bhawana ___ gmx-users mailing listgmx-users@gromacs.org http://w

[gmx-users] peptide goes out of box after md simulation

hello everyone, After doing md simulation with no. of steps 1 ns ,my peptide which is of 7-8 residue move out of the boundary of water box. tell me what shd i do get rid of this problem. Also i want to know about the wall of the box, whether it is permeable or semi-permiable. this is very silly q

[gmx-users] grace/xmgace

hello everyone, i m getting problem with in finding grace as instead of default path. My path is home/bhawana/gromacs/bin/.. so i have to plot my .xvg files by using xmgrace but i m not getting where it is otherwise by default its path is /usr/local/grace/bin/xmgrace. what shd i do. whether there

[gmx-users] Re: Re: .top

hello everyone, thankyou for your reply. if interchanging water topolgy and position restraint position,mean that it is being applied to water, not the molecule. Then what should i do so that i dont get error when i put it in order of #include "ffgmx.itp" #include "boc.itp" #include "spc.itp" #i

[gmx-users] .top file

hello everyone, while doing grompp for prest by giving command grompp -f *_md_water_prest.mdp -c *_md_water_em.gro -p *.top -o *_md_water_prest.tpr *i get the error* -- Program grompp, VERSION 4.0 Source code file: toppush.c, line: 1196 Fatal e

[gmx-users] gro file

hello everyone, i m having a peptide of 3 residue named Boc-BetaAla-Aib-OMe made from prodrg server when i give the grompp command for vacuum i.e. grompp -f boc1_vac_st.mdp -c boc1.gro -p boc1.top -o boc1_vac_st.tpr i got an error: ERROR: The cut-off length is longer than half the shortest box vec

Re: [gmx-users] missing of methyl at N-terminal

hello, thankyou for ur advice on the mail named *missing of methyl at N-terminal. * i m using forcefield ffgmx. u had advice me to put the correct name for terminal N-CH3 group i.e. i had replaced NHM with NAC as given there. That error has been solved but again i m getting the error as:

[gmx-users] posre.itp

hello everyone, Pls tell me from where i can get posre.itp means format of this file. Here in one mail named topology, you had given solution for making pdb file from one other than PRODRG i.e. Build a small one by hand in a text editor (making sure the density is suitable and there won't be ster

[gmx-users] position restraint and pdb

hello everyone, pls tell me that whether we can use gromacs for simulating pdb with 3 or 4 residue. As i had done it with 4 residue with blocking group. But then i got the error for rvdw and rlist as they should be nearer to cutoff value. So instead of decreasing the value of rvdw. i increased my

[gmx-users] about porse.itp

Dear gmx-users, i made earlier asked this question .but there is a problem. first i got the error: --- Program grompp, VERSION 4.0 Source code file: futil.c, line: 527 Fatal error: Library file posre.itp not found in current dir nor in default

[gmx-users] prodrg

hello everyone, Pls tell me whether we can use PRODRG server only for generating peptides with unusual amino acid through JME or it can be used for the peptides having usual amino acid. whether it is necessary to use pdb2gmx for peptide containing usual amino acid or we can do it with PRODRG serve

Re: [gmx-users] missing of methyl at N-terminal

thankyou for ur reply. exact error which i m getting, when running pdb2gmx command with the pdb which i had taken from insightII is Program pdb2gmx, VERSION 4.0 Source code file: pdb2gmx.c, line: 429 Fatal error: Atom C in residue NH2 6 not found in rtp entry with 3 atoms while sortin

[gmx-users] missing of methyl at N-terminal

hello everyone, for doing peptide with usual amino acid simulation. i m bringing my *.pdb file from insightII as i dont know any other tool or software from where i can get any pdb file (model peptide-Eg. Ac-Ala-Ala-Ala-Ala-NHMe).But when i put my pdb file in gromacs by using pdb2gmx. it give err

[gmx-users] how much ns-one more question

thanks for reply. but sir, when i start it with 1ns md simulation,my peptide doesnot get stable because it was moving in zigzag like motion. so should i go for 5 ns or not. which ns means (1ns or 2ns...20ns) is better so that i can get good results. with regards Bhawana ___

[gmx-users] problem

Sir, thankyou for reply i m just getting started to Gromacs but i have included porse.itp in my topology file. i m not getting that what does this mean that it is not present in the current directory. whether i had to make porse.itp file and then save in my current directory. Also tell me what is

[gmx-users] how much ns

hi, i want to ask that how we can know that how much ns(1 ns or 2 ns.20 ns), we can run on our system which doing md simulations. Means how we cme to know that if we go for 5 ns, then our system will not hang or crash out. Please help me. with regards Bhawana ___

[gmx-users] problem in prest.mdp file

me as soon as possible. With Regards Bhawana Gupta ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't pos

[gmx-users] problem

through mail, i got nothing Kindly help me solve this problem. With Regards Bhawana Gupta ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before p

[gmx-users] problem in em.mdp file

s not a real value while googling through mail, i got nothing Kindly help me solve this problem. With Regards Bhawana Gupta ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at ht