Re: [gmx-users] Error in pdb2gmx

On 4/30/13 6:10 AM, Nikunj Maheshwari wrote: Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message ("Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ") when I used OPL

Re: [gmx-users] Error in pdb2gmx

Thanks Justin. I know that using -ignh will solve the problem. But I was just curious because I got the same error message ("Fatal error: Atom HD1 in residue HIS 65 was not found in rtp entry HISE with 17 atoms while sorting atoms. ") when I used OPLS, this time it was His 65. So I used -his optio

Re: [gmx-users] Error in pdb2gmx

On 4/30/13 2:59 AM, Nikunj Maheshwari wrote: Dear all, I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o output.gro) I used 13. GROMOS 53a6 force field "Fatal error: Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while sorting atoms. For a hydrogen, th

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Thats great. I am able to make now my 1A8G.itp file and also the CG structure of protein but now the other problem which is arising is to make the topol.top file and conf.gro file. When I am making this using the command...pdb2gmx -v -f 1A8G_CG.pdb -o conf.gro -p topol.top .

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Hi Justin, Thanks for the expedient reply. I referred MARTINI but after converting 1A8G.pdb to 1A8G_CG.pdb i.e. CG structure of protein I dnt know how to make the topol.top and conf.gro files for that and also I am not able to generate the posre.itp file with this CG struct

Re: [gmx-users] Error in PDB2GMX

sunny mishra wrote: Hi, I am working on HIV-1 Protease with PDB ID 1A8G.pdb. I am trying to convert this protein structure to COARSE GRAINED protein structure and I am done with that but when I am trying to make the topology and conf.gro file from my CG structure of 1A8G.pdb using pdb2gmx it

Re: [gmx-users] Error in pdb2gmx

Robert Kretschmer wrote: Dear all, i have a problem while running pdb2gmx. I want to run a md simulation with HIV-ReverseTranscriptase (PDB: 1TVR & 1HNV). But in pdb2gmx i get the following error: "Fatal error: Incomplete ring in HIS221" I checked HIS221 and found, that it should be an

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

lt;mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> <mailto:[EM

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

sharma <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

EMAIL PROTECTED]>> >> >>Dear Vivek, >>you just have to download swisspdb and open your pdb file. Thats all >>you got to do and It is more than enough. If you have more than 2/3 >> residues missing then, make sure the Ramachandran plots are fine. >>Als

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

ECTED]>>/* wrote: From: vivek sharma <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: "Discussion list for GROMACS users" mailto

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

to do and It is more than enough. If you have more than 2/3 residues >> missing then, make sure the Ramachandran plots are fine. Also try a simple >> minimization before begining gromacs. >> >> nahren >> >> --- On *Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]>* wro

Re: [gmx-users] Error in pdb2gmx

Hi Vivek, I downloaded 3bzu.pdb and ran the sorting on it as I described before (sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}' 3bzu.pdb | sort | cut -b 2-), and it worked perfectly for me. I don't see how you'd end up with some atoms inbetween other residues. It seems as

Re: [gmx-users] Error in pdb2gmx

Hi Vivek, Sorry, I should've been more careful. Sorting will obviously take the rest of the line in account. I'll send a proper solution in a few moments... Cheers, Tsjerk On Wed, Aug 13, 2008 at 7:33 AM, vivek sharma <[EMAIL PROTECTED]> wrote: > Thanx David and Tsjerk, > I tried the option g

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

n *Tue, 8/12/08, vivek sharma <[EMAIL PROTECTED]>* wrote: > > From: vivek sharma <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue > PHE270 while adding hydrogens > To: "Discussion list for GROMACS users" > Dat

Re: [gmx-users] Error in pdb2gmx

Thanx David and Tsjerk, I tried the option given by Tsjerk on pdb file, then pdb2gmx command on sorted pdb file was giving the following error. Sorting it all out... Opening library file /usr/share/gromacs/top/ffG43a1.hdb Opening library file /usr/share/gromacs/top/ffG43a1-n.tdb Opening library

Re: [gmx-users] Error in pdb2gmx

Well, sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}' file.pdb | sort | cut -b 2- > sorted.pdb sort of seems to do the trick. But it will place the chainless things first. Hope it helps, Tsjerk On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

/12/08, vivek sharma <[EMAIL PROTECTED]> wrote: From: vivek sharma <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Error in pdb2gmx.Atom CE2 not found in residue PHE270 while adding hydrogens To: "Discussion list for GROMACS users" Date: Tuesday, August 12, 2008, 6:34 PM

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

If atoms are missing in the sidechains of your protein, you can try a program like scwrl3 to rebuild all or some of the sidechains. This will give you complete sidechains in sort of reasonable positions. Cheers /Per 12 aug 2008 kl. 15.04 skrev vivek sharma: Hi David, Thanx a lot again.

Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. The chain identifier needs to be continuous. That is, if you have atoms with chain identifiers like: A A B A C A A they should be re-written as: A A A A A B C This can be a

Re: [gmx-users] Error in pdb2gmx

Hi david, Thanx again, but I want to ask what changes need to be done there in such cases. With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >> Hi David, >> Thanks for the quick reply. My apologies for asking you again a silly >> doubt as, I am doing thi

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

Hi David, Thanx a lot again. can you please tell me the criteria or the standards to do such correction or can you suggest some link or tutorial for the same? whether swiss pdb can help in such cases? With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wrote: > >

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error.

Re: [gmx-users] Error in pdb2gmx.....Atom CE2 not found in residue PHE270 while adding hydrogens

vivek sharma wrote: Hi There, I am new to molecular dynamics and GROMACS. While trying MD for 1XU9.pdb (pdbid) in the very 1st step on using the command pdb2gmx -f 1XU9.pdb -o 1XU9.gro -p 1XU9.top -i 1XU9.itp -vsite hydrogen -water spce I got the following in the last of error. ..

Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. with a text editor, like emacs, notepad or whatever. With Tha

Re: [gmx-users] Error in pdb2gmx

Hi David, Thanks for the quick reply. My apologies for asking you again a silly doubt as, I am doing this all for the first time. It will be of great help if you can tell me how to do such correction manually. With Thanx, Vivek 2008/8/12 David van der Spoel <[EMAIL PROTECTED]> > vivek sharma wro

Re: [gmx-users] Error in pdb2gmx

vivek sharma wrote: Hello there, I am trying to run pdb2gmx on 3bzu.pdb file and got the following error Opening library file /usr/share/gromacs/top/ ffG43b1.rtp Opening library file /usr/share/gromacs/top/aminoacids.dat Reading 3bzu.pdb... WARNING: all CONECT records are ignored Read 'CORTICOST

Re: [gmx-users] error in pdb2gmx

Dmitriy Golubobsky wrote: Please, give an adive. I've add new residues to ffoplsaa.rtp build pdb file. and try to convert it to gromacs format. under WindowsXP, using GROMACS 3.2.1 everyting is OK. but, when i did the same comman under GROMACS 3.3.1 (SuSE), i've got an error: Read 4904 atoms Op

Re: [gmx-users] error in pdb2gmx step

True. I checked the files and found that CO was not described in any of them and I did take care of the replacement ot A with a blank.  Well in this case do I have any alternatives? Like other compatible force fields or modification of the existing one. Annie Albin. On 3/31/06, MGiò <[EMAIL PROTE

Re: [gmx-users] error in pdb2gmx step

That means that the CO ion type is not described by the forcefield you are using, check the .rtp file of your force field or the ions.itp file in the gromacs/top directory. anyhow be careful not to make any confusion between the chain identifier, which is a 1 character id, and the residue name. Are

Re: [gmx-users] error in pdb2gmx step

Well thank you.Yes I did find a region in which chain identifier 'A' was repeating, this corresponded to the HETATM CO, so i tried removing the chain identifier in one case and in another one I tried shifting it to the correspoding chain, but in both cases i got the following error "Fatal error: R

Re: [gmx-users] error in pdb2gmx step

Hi!it seems that pdb2gmx has detected an interruption in your chain A numbering, are you sure that there are none? or else are you sure that you're not using the same chain id for more than one chain? for example for two different monomers? hope it helps,MGOn 3/31/06, Annie Albin < [EMAIL PROTECTED

Re: [gmx-users] error in pdb2gmx step

Check you pdb file and see if the chain identifier A occurs at different places in the file. Pdb2gmx expects a chain to be continous, and if it isn't, it gets confused. If you have several chains, rename them accordingly. Cheers /Per Annie Albin wrote: Dear all, I faced a problem in the