[gmx-users] sulfate in topology file with oplsaa forcefield

Dear users, I have to complete my topology file and there is sulfate(SO4(-2)) in pdb file. But I don't know how can I complete this file with oplsaa forcefield. I can't find so4 in ffopls.tpr file. I would really appropriate if you could do this for me. thank you

[gmx-users] Re: vdwtype=shift

11 of gromacs manual (v4.0)/ -Gaurav On Thu, Jun 24, 2010 at 4:40 AM, Erik Marklund wrote: > you zou skrev: >> >> Dear users, >> >> I have a question about vdwtype. My question is if I use vdwtype=shift in >> nvt.mdp file: >> >> ; Neighborsearchin

[gmx-users] vdwtype=shift

Dear users, I have a question about vdwtype. My question is if I use vdwtype=shift in nvt.mdp file: ; Neighborsearchingns_type = grid ; search neighboring grid celsnstlist = 5 ; 10 fsrlist= 1.0 ; short-range neighborlist cutoff (

[gmx-users] Incomplete ring

Hi again,Thank you, I added missing atoms with emacs, but my question is this ring doesn't have to be complete and if I add missing atoms with HIS680's name, I change its structure. Is it true? > Hi Users, > > I have a .pdb file, in this file when I want to use pdb2gmx command > there is this er

[gmx-users] Incomplete ring

Hi Users, I have a .pdb file, in this file when I want to use pdb2gmx command there is this error massage:Fatal error:Incomplete ring in HIS680 this aminoacid is not complete in general, I don't know how can I complete this such that I don't add HIS for complete? Please give me a hint. Thank you

[gmx-users] [pairs] and [dihedrals]

Hi everyone, I have one question about topology, If I want to write topology by hand, how can I write pairs and dihedrals without mistakes? Is there any free softwares to use? Thank you _ Hot

[gmx-users] write topology by hand

Hi everyone, I had a .pdb file that was drug_enzyme complex. Drug was GOL(Glycerol) and I wrote topology file by hand but now when I run grompp command I have this error:Fatal error:Syntax error - File ffoplsaabon.itp, line 4Last line read:'[ bondtypes ]'Invalid order for directive bondtypes an

[gmx-users] add missing atom(s)

Hi,Which tool(s) is/are useful? I don't have any idea for this problem.Thank you you zou wrote: > Hi again, > > Sorry, in "REMARK 470" there is: > > REMARK 470 > > REMARK 470 MISSING ATOM > > REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=

[gmx-users] add missing atoms

Hi again,Sorry, in "REMARK 470" there is:REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES

[gmx-users] add missing atom

Hi everyone, I have one question about adding atoms that are missing in residue. This atom is OG in SER amino acid. I don't know how can I add this atom to my residue. If I have to add this atom manually how can I find coordinates of that? Or If there is server or software to do this I will be

[gmx-users] OPLS-AA forcefield

Hi everyone, I have one simple question. I don't know is there any different between OPLS-AA forcefield and OPLS-AA/L forcefield? I think these are different but when I use pdb2gmx tool there is no OPLS-AA forcefield to choose. Thank you _

[gmx-users] Re: OPLS-AA/L force field

propriate structure. If you need additional hydrogens, the Gromacs "protonate" tool can generate an all-atom structure. -Justin > Thanks, > > > > you zou wrote: >> Hi again, >> >> Sorry I confused you with my question. My question is How can I make

[gmx-users] Re: OPLS-AA/L force field

can handle .pdb, How can it do this, because number of atoms are different(Which command I have to use?). If can't handle it how can I add Hydrogens to drg.gro?Thanks, you zou wrote: > Hi again, > > Sorry I confused you with my question. My question is How can I make .gro > file

[gmx-users] Re: OPLS-AA/L force field

command I will miss something, is it true?Thank you again you zou wrote: > Hi Justin, > > Thank you for your help, But when I run x2top command there is one error > that is: > " > Can not find forcefield for atom C1-1 with 2 bonds > Can not find forcefield for atom C4-4 wi

[gmx-users] Re: OPLS-AA/L force field

ind a forcefield type for 6 out of 24 atoms"I don't know how can I adjust this error.I have one more question again, this command give me a top file, if I want gro file of this pdb (drug that has removed from drug-enzyme complex) how can I do that? you zou wrote: > Dear Users, >

[gmx-users] OPLS-AA/L force field

Dear Users, I have one question about Drug-Enzyme Complex,Similar to tutorial If I want to use GROMOS96 43a1, I can use "Prodrg Beta version" for drug but If I want to use OPLS-AA/L all-atom force field I can use "Prodrg Beta version" server too, or not?If I can't use this server, how can I mak

[gmx-users] remove from mailing list

Hi All, I send you an email that now I want to remove/delete that but I do't now.my question is how can I remove my email? Thank you _ Hotmail: Trusted email with powerful SPAM protection. htt