Dear Mark Abraham,<br><br>Thank you for your support. However, I have edited the N-terminus in -hdb file so as too include a HN atom for the specific residue and it worked.<br><br>regards,<br>Uday..<br><br><div class="gmail_quote">
On Fri, Jun 17, 2011 at 10:29 PM, <span dir="ltr"><<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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Today's Topics:<br>
<br>
1. cyclic peptide on GROMACS compatoble with Charmm (all-atom)<br>
force field (udaya kiran marelli)<br>
2. Re: gmx4.5.4 genion problem: No line with moleculetype 'SOL'<br>
found (Ye Yang)<br>
3. gmx4.5.4 genion problem: No line with moleculetype 'SOL'<br>
found (<a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>)<br>
4. Re: cyclic peptide on GROMACS compatoble with Charmm<br>
(all-atom) force field (Mark Abraham)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Fri, 17 Jun 2011 17:13:54 +0200<br>
From: udaya kiran marelli <<a href="mailto:kiran.udaya@gmail.com">kiran.udaya@gmail.com</a>><br>
Subject: [gmx-users] cyclic peptide on GROMACS compatoble with Charmm<br>
(all-atom) force field<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw@mail.gmail.com">BANLkTikpHYWX3Vf2irw7zZyF00VDwM5qyw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear GROMACS users,<br>
<br>
I am trying to construct a cyclic hexa peptide containing all Ala residues.<br>
During pdb2gmx conversion using the command (pdb2gmx -ff charmm27 -ignh<br>
-f TESTALA.pdb -o TESTALA.gro -ter) it gave the following error while I am<br>
demanding the program to give uncharged termini (option : None)<br>
<br>
WARNING: atom HN is missing in residue ALA 1 in the pdb file<br>
You might need to add atom HN to the hydrogen database of residue<br>
ALA<br>
in the file ff???.hdb (see the manual)<br>
<br>
<br>
-------------------------------------------------------<br>
Program pdb2gmx, VERSION 4.0.5<br>
Source code file: pdb2top.c, line: 704<br>
<br>
Fatal error:<br>
There were 1 missing atoms in molecule Protein, if you want to use this<br>
incomplete topology anyhow, use the option -missing<br>
<br>
In the .hdb file the atom HN is defined already. The error is that it is<br>
removing the #HN# atom from the Ala 1 residue at the cyclization point.<br>
<br>
Could you suggest me in getting rid off the problem.<br>
<br>
<br>
yours sincerely<br>
Uday.<br>
<br>
Marelli Udaya Kiran<br>
C/o. Professor Dr. Horst Kessler<br>
Institute for Advanced Study<br>
Department Chemie<br>
Technische Universität München<br>
Lichtenbergstrasse 4<br>
D-85747 Garching, Germany<br>
<br>
Tel.: <a href="tel:%2B49-%280%2989-289-13760" value="+498928913760">+49-(0)89-289-13760</a><br>
Fax: <a href="tel:%2B49-%280%2989-289-13210" value="+498928913210">+49-(0)89-289-13210</a><br>
email: <a href="mailto:kiran.udaya@tum.de">kiran.udaya@tum.de</a><br>
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Message: 2<br>
Date: Fri, 17 Jun 2011 13:06:44 -0400<br>
From: Ye Yang <<a href="mailto:knightyangpku@gmail.com">knightyangpku@gmail.com</a>><br>
Subject: Re: [gmx-users] gmx4.5.4 genion problem: No line with<br>
moleculetype 'SOL' found<br>
To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
<<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:BANLkTinRa2ff2aBDnWcBbKKX0FTZNWyiKw@mail.gmail.com">BANLkTinRa2ff2aBDnWcBbKKX0FTZNWyiKw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Thank you for your suggestions.<br>
I have checked the topology file with vim, and it looks pefectly, also, the<br>
only problem happens when I use genion. One thing that might be possible is<br>
that I use the double precision version of gromacs, because when I solve it<br>
in water, the written of topology file looks weired(like I showed).<br>
What do you mean by work-around? You mean just manually change some water<br>
molecules in topology file and coordinate file into ions? Will the program<br>
recognize something like CL, NA? Or can I just add ions to the system and<br>
solve it in water?<br>
<br>
Thank you very much<br>
<br>
Best<br>
Wishes<br>
<br>
Ye<br>
<br>
2011/6/16 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>
<br>
><br>
><br>
> Ye Yang wrote:<br>
><br>
>> Hi, everyone:<br>
>> I am a new user of Gromacs, and I am running through the tutorial.<br>
>> When I am trying to run the ligand-receptor binding tutorial from<br>
>><br>
>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html</a><br>
>> I met some trouble in adding ion.<br>
>> Each time when I use genion, it shows:<br>
>><br>
>> Will try to add 0 NA ions and 6 CL ions.<br>
>> Select a continuous group of solvent molecules<br>
>> Group 0 ( System) has 33046 elements<br>
>> Group 1 ( Protein) has 1693 elements<br>
>> Group 2 ( Protein-H) has 1301 elements<br>
>> Group 3 ( C-alpha) has 163 elements<br>
>> Group 4 ( Backbone) has 489 elements<br>
>> Group 5 ( MainChain) has 653 elements<br>
>> Group 6 ( MainChain+Cb) has 805 elements<br>
>> Group 7 ( MainChain+H) has 815 elements<br>
>> Group 8 ( SideChain) has 878 elements<br>
>> Group 9 ( SideChain-H) has 648 elements<br>
>> Group 10 ( Prot-Masses) has 1693 elements<br>
>> Group 11 ( non-Protein) has 31353 elements<br>
>> Group 12 ( Other) has 15 elements<br>
>> Group 13 ( JZ4) has 15 elements<br>
>> Group 14 ( Water) has 31338 elements<br>
>> Group 15 ( SOL) has 31338 elements<br>
>> Group 16 ( non-Water) has 1708 elements<br>
>> Select a group: 15<br>
>> Selected 15: 'SOL'<br>
>> Number of (3-atomic) solvent molecules: 10446<br>
>><br>
>> Processing topology<br>
>><br>
>> Back Off! I just backed up temp.top to ./#temp.top.3#<br>
>><br>
>> -------------------------------------------------------<br>
>> Program genion_d, VERSION 4.5.4<br>
>> Source code file: gmx_genion.c, line: 285<br>
>><br>
>> Fatal error:<br>
>> No line with moleculetype 'SOL' found the [ molecules ] section of file<br>
>> 'topol.top'<br>
>><br>
>><br>
> Something doesn't match up here - the command backs up temp.top, but then<br>
> complains it can't find SOL in topol.top. Either genion is looking at the<br>
> wrong file or your command is somehow wrong.<br>
><br>
><br>
> I checked my topology file and it looks fine:<br>
>> ; Include Position restraint file<br>
>> #ifdef POSRES<br>
>> #include "posre.itp"<br>
>> #endif<br>
>><br>
>> ; Include water topology<br>
>> #include "gromos43a1.ff/spc.itp"<br>
>><br>
>> ; Include ligand topoloty<br>
>> #include "drg.itp"<br>
>> #ifdef POSRES_WATER<br>
>> ; Position restraint for each water oxygen<br>
>> [ position_restraints ]<br>
>> ; i funct fcx fcy fcz<br>
>> 1 1 1000 1000 1000<br>
>> #endif<br>
>><br>
>> ; Include topology for ions<br>
>> #include "gromos43a1.ff/ions.itp"<br>
>><br>
>> [ system ]<br>
>> ; Name<br>
>><br>
>> Protein<br>
>> [ molecules ]<br>
>> ; Compound #mols<br>
>> Protein_chain_A 1<br>
>> JZ4 1 SOL 10446<br>
>><br>
>> One thing that might happen is in the genion source file, I read through<br>
>> it, and the problem either happens in loading the line to buf2, or in the<br>
>> gmx_strcmp(buf2,"SOL"), since clearly the SOL_line is -1 aftermath.<br>
>><br>
>> The other thing I tried is to remove the ligand JZ4 part in both topology<br>
>> and coordinates file, and in this case, it works perfectly for adding ion.<br>
>> But in this way, I do not know how to insert my ligand into the system since<br>
>> it might collide with solvent.<br>
>><br>
>><br>
> If removal of the JZ4 line relieves the problem, perhaps there's a problem<br>
> with that line, i.e. the line ending? What type of system are you using?<br>
> Sometimes Windows line endings cause problems. Always use a plain text<br>
> editor and use dos2unix to process text files if you're on Windows.<br>
><br>
> Otherwise, the work-around is to not have genion work on the topology.<br>
> Make the corrections yourself. Simple addition of ions and subtraction of<br>
> water molecules is trivial.<br>
><br>
> -Justin<br>
><br>
><br>
> Can someone help me with this problem?<br>
>><br>
>> Thank you all very much.<br>
>><br>
>> Ye Yang<br>
>><br>
>><br>
>><br>
> --<br>
> ========================================<br>
><br>
> Justin A. Lemkul<br>
> Ph.D. Candidate<br>
> ICTAS Doctoral Scholar<br>
> MILES-IGERT Trainee<br>
> Department of Biochemistry<br>
> Virginia Tech<br>
> Blacksburg, VA<br>
> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080">(540) 231-9080</a><br>
><br>
> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
><br>
> ========================================<br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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Message: 3<br>
Date: Fri, 17 Jun 2011 16:04:54 -0400<br>
From: <a href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a><br>
Subject: [gmx-users] gmx4.5.4 genion problem: No line with<br>
moleculetype 'SOL' found<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
Message-ID: <<a href="mailto:20110617160454.y27k51qt1k4oc848@webmail.utoronto.ca">20110617160454.y27k51qt1k4oc848@webmail.utoronto.ca</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";<br>
format="flowed"<br>
<br>
For the quick fix:<br>
<br>
1. run genion on your topology that does work. Look at this to see the<br>
format of the ion atom and residue names<br>
<br>
2. Pick a few waters in the structure containing the ligand and<br>
replace the OW by the ion and remove the hydrogens, then fix the<br>
number of atoms on the second line of the file and run editconf on the<br>
file.<br>
<br>
** But I wouldn't be satisfied with that if I were you. there is some<br>
problem here that you should uncover now before you move farther.<br>
<br>
Show us your commands exactly (copy and paste) and perhaps we can help more.<br>
<br>
As a side note: your topology that you presented is going to cause<br>
you problems if you try to put position restraints on the water, as it<br>
is incorrectly ordered:<br>
<br>
; Include water topology<br>
#include "gromos43a1.ff/spc.itp"<br>
<br>
; Include ligand topoloty<br>
#include "drg.itp"<br>
#ifdef POSRES_WATER<br>
; Position restraint for each water oxygen<br>
[ position_restraints ]<br>
; i funct fcx fcy fcz<br>
1 1 1000 1000 1000<br>
#endif<br>
<br>
<br>
-- original message --<br>
<br>
Thank you for your suggestions.<br>
I have checked the topology file with vim, and it looks pefectly, also, the<br>
only problem happens when I use genion. One thing that might be possible is<br>
that I use the double precision version of gromacs, because when I solve it<br>
in water, the written of topology file looks weired(like I showed).<br>
What do you mean by work-around? You mean just manually change some water<br>
molecules in topology file and coordinate file into ions? Will the program<br>
recognize something like CL, NA? Or can I just add ions to the system and<br>
solve it in water?<br>
<br>
Thank you very much<br>
<br>
Best<br>
Wishes<br>
<br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Sat, 18 Jun 2011 06:29:39 +1000<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] cyclic peptide on GROMACS compatoble with<br>
Charmm (all-atom) force field<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4DFBB933.2010806@anu.edu.au">4DFBB933.2010806@anu.edu.au</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
On 18/06/2011 1:13 AM, udaya kiran marelli wrote:<br>
> Dear GROMACS users,<br>
><br>
> I am trying to construct a cyclic hexa peptide containing all Ala<br>
> residues. During pdb2gmx conversion using the command (pdb2gmx -ff<br>
> charmm27 -ignh -f TESTALA.pdb -o TESTALA.gro -ter) it gave the<br>
> following error while I am demanding the program to give uncharged<br>
> termini (option : None)<br>
><br>
> WARNING: atom HN is missing in residue ALA 1 in the pdb file<br>
> You might need to add atom HN to the hydrogen database of<br>
> residue ALA<br>
> in the file ff???.hdb (see the manual)<br>
<br>
With -ignh you told it to strip away all the H atoms, and that requires<br>
that pdb2gmx knows how to rebuild them (or doesn't need to know).<br>
<br>
> -------------------------------------------------------<br>
> Program pdb2gmx, VERSION 4.0.5<br>
> Source code file: pdb2top.c, line: 704<br>
><br>
> Fatal error:<br>
> There were 1 missing atoms in molecule Protein, if you want to use<br>
> this incomplete topology anyhow, use the option -missing<br>
><br>
> In the .hdb file the atom HN is defined already. The error is that it<br>
> is removing the #HN# atom from the Ala 1 residue at the cyclization point.<br>
<br>
If you mean that the the cyclization is achieved with a peptide bond<br>
from "N-terminal" N to "C-terminal" C, you will have to use the<br>
specbond.dat mechanism to achieve that. See chapter 5.<br>
<br>
The problem arises because HN is defined in the .hdb in terms of C in<br>
the preceding residue, which is not applicable in your case, because<br>
there is not a regular peptide bond.<br>
<br>
Rather than the "brute force" -ignh mechanism, there may be a better<br>
approach (like removing particular offending hydrogen atoms from your<br>
input coordinate file) that doesn't require pdb2gmx to need to know how<br>
to rebuild HN.<br>
<br>
Mark<br>
<br>
> Could you suggest me in getting rid off the problem.<br>
><br>
><br>
> yours sincerely<br>
> Uday.<br>
><br>
> Marelli Udaya Kiran<br>
> C/o. Professor Dr. Horst Kessler<br>
> Institute for Advanced Study<br>
> Department Chemie<br>
> Technische Universität München<br>
> Lichtenbergstrasse 4<br>
> D-85747 Garching, Germany<br>
><br>
> Tel.: <a href="tel:%2B49-%280%2989-289-13760" value="+498928913760">+49-(0)89-289-13760</a> <tel:%2B49-%280%2989-289-13760><br>
> Fax: <a href="tel:%2B49-%280%2989-289-13210" value="+498928913210">+49-(0)89-289-13210</a> <tel:%2B49-%280%2989-289-13210><br>
> email: <a href="mailto:kiran.udaya@tum.de">kiran.udaya@tum.de</a> <mailto:<a href="mailto:kiran.udaya@tum.de">kiran.udaya@tum.de</a>><br>
><br>
<br>
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