Addition to Dan:
What's about CC CXX?
Hai Nguyen
> On Mar 9, 2017, at 8:48 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> What version of GNU compilers are you using? What are the options you
> are passing to configure? Although in your initial post you say you
> are trying to compile with gcc, your error message makes it look like
> you're really using clang.
>
> -Dan
>
>> On Thu, Mar 9, 2017 at 8:45 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>> Hi,
>>
>> thank you for your answer.
>>
>> I am using the last release version of AmberTools available on the
>> official website (AmberTools16)
>>
>> I need parmed and openmm for computing the potential energy of a small
>> peptide (succeedly installed). While parmed alone allows me to load the
>> force fields parameters, computing the potential energy of a molecule
>> fails because the topology of the molecule is not loaded.
>>
>> It seems that the only way is to load the topology from the prmtop file,
>> this is why I need to compile AmberTools, or at least the leap
>> executables for building such file.
>>
>>
>> Tom.
>>
>>> On 03/09/2017 02:33 PM, Daniel Roe wrote:
>>> Hi,
>>>
>>> Which version of AmberTools are you using?
>>>
>>> Also, if all you need is parmed you can always get it straight from
>>> GitHub: https://github.com/ParmEd/ParmEd
>>>
>>> -Dan
>>>
>>> On Thu, Mar 9, 2017 at 8:04 AM, Tom Dreyfus <tom.dreyfus.inria.fr> wrote:
>>>>> Dear Amber developpers,
>>>>>
>>>>> We are very much interested in using the Amber force field. Of
>>>>> particular interest is the Python library Parmed
>>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>>> accessing the potential energy terms one by one.
>>>>>
>>>>> We need to generate the prmtop files, which requires the AmberTools suite.
>>>>>
>>>>> We have followed the steps described in the installation
>>>>> documentation, but unfortunately did not succeed to build the tools. I
>>>>> have got the following errors i am stuck with (see below).
>>>>>
>>>>> I am using Fedora 23 and try to compile using gcc.
>>>>>
>>>>> Can you please guide us on how to compile the tools ?
>>>>>
>>>>> Thank you for your attention.
>>>>>
>>>>> Tom.
>>>>>
>>>>> *In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>>> error: conflicting types for 'memchr'**
>>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>>> error: conflicting types for 'strchr'**
>>>>> ** strchr(char* __s, int __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>>> **extern char *strchr (const char *__s, int __c)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>>> error: conflicting types for 'strpbrk'**
>>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>>> error: conflicting types for 'strrchr'**
>>>>> ** strrchr(char* __s, int __n)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>>> **extern char *strrchr (const char *__s, int __c)**
>>>>> ** ^**
>>>>> **In file included from pdb_type.cpp:29:**
>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>>> error: conflicting types for 'strstr'**
>>>>> ** strstr(char* __s1, const char* __s2)**
>>>>> ** ^**
>>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>>> ** ^**
>>>>> **5 errors generated.*
>>>>>
>>>>> AND
>>>>>
>>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o CliqueList.o
>>>>> AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o -L../libpdb -lpdb++
>>>>> -L../toolclasses -ltoolclasses -lm **
>>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>>> invocation)**
>>>>> **Makefile:41: recipe for target 'reduce' failed*
>>>> On 03/09/2017 02:02 PM, Tom Dreyfus wrote:
>>>>>> Dear Amber developpers,
>>>>>>
>>>>>> We are very much interested in using the Amber force field. Of
>>>>>> particular interest is the Python library Parmed
>>>>>> (https://parmed.github.io/ParmEd/html/amber.html), as it allows
>>>>>> accessing the potential energy terms one by one.
>>>>>>
>>>>>> We need to generate the prmtop files, which requires the AmberTools
>>>>>> suite.
>>>>>>
>>>>>> We have followed the steps described in the installation
>>>>>> documentation, but unfortunately did not succeed to build the tools.
>>>>>> I have got the following errors i am stuck with (see below).
>>>>>>
>>>>>> I am using Fedora 23 and try to compile using gcc.
>>>>>>
>>>>>> Can you please guide us on how to compile the tools ?
>>>>>>
>>>>>> Thank you for your attention.
>>>>>>
>>>>>> Tom.
>>>>>>
>>>>>> *In file included from pdb_type.cpp:29:**
>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:100:3:
>>>>>> error: conflicting types for 'memchr'**
>>>>>> ** memchr(void* __s, int __c, size_t __n)**
>>>>>> ** ^**
>>>>>> **/usr/include/string.h:92:14: note: previous declaration is here**
>>>>>> **extern void *memchr (const void *__s, int __c, size_t __n)**
>>>>>> ** ^**
>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:104:3:
>>>>>> error: conflicting types for 'strchr'**
>>>>>> ** strchr(char* __s, int __n)**
>>>>>> ** ^**
>>>>>> **/usr/include/string.h:231:14: note: previous declaration is here**
>>>>>> **extern char *strchr (const char *__s, int __c)**
>>>>>> ** ^**
>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:108:3:
>>>>>> error: conflicting types for 'strpbrk'**
>>>>>> ** strpbrk(char* __s1, const char* __s2)**
>>>>>> ** ^**
>>>>>> **/usr/include/string.h:310:14: note: previous declaration is here**
>>>>>> **extern char *strpbrk (const char *__s, const char *__accept)**
>>>>>> ** ^**
>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:112:3:
>>>>>> error: conflicting types for 'strrchr'**
>>>>>> ** strrchr(char* __s, int __n)**
>>>>>> ** ^**
>>>>>> **/usr/include/string.h:258:14: note: previous declaration is here**
>>>>>> **extern char *strrchr (const char *__s, int __c)**
>>>>>> ** ^**
>>>>>> **In file included from pdb_type.cpp:29:**
>>>>>> **/usr/bin/../lib/gcc/x86_64-redhat-linux/5.3.1/../../../../include/c++/5.3.1/cstring:116:3:
>>>>>> error: conflicting types for 'strstr'**
>>>>>> ** strstr(char* __s1, const char* __s2)**
>>>>>> ** ^**
>>>>>> **/usr/include/string.h:337:14: note: previous declaration is here**
>>>>>> **extern char *strstr (const char *__haystack, const char *__needle)**
>>>>>> ** ^**
>>>>>> **5 errors generated.*
>>>>>>
>>>>>> AND
>>>>>>
>>>>>> */usr/bin/clang++ -o reduce GraphToHoldScores.o reduce.o CTab.o
>>>>>> ElementInfo.o StdResH.o ResBlk.o AtomConn.o AtomPositions.o DotSph.o
>>>>>> Mover.o RotMethyl.o RotAromMethyl.o RotDonor.o FlipMemo.o
>>>>>> CliqueList.o AtomDescr.o PDBrec.o MoveableNode.o hybrid_36_c.o
>>>>>> -L../libpdb -lpdb++ -L../toolclasses -ltoolclasses -lm **
>>>>>> **/usr/bin/ld: cannot find -lpdb++**
>>>>>> **clang: error: linker command failed with exit code 1 (use -v to see
>>>>>> invocation)**
>>>>>> **Makefile:41: recipe for target 'reduce' failed*
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>>>
>>>
>>
>>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
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Received on Thu Mar 09 2017 - 06:00:05 PST
